Experiment: 2BD2

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3EST

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	294	25MM SODIUM SULPHATE, 25MM SODIUM ACETATE (PH 5.0), 25 MG/ML PPE AND 17.5 MG/ML BCM7, AND THEN SOAKED WITH ARG-PHE (2MG) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 45 MIN, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.02	39.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.195	α = 90
b = 57.883	β = 90
c = 74.605	γ = 90

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	127	IMAGE PLATE	RIGAKU RAXIS IV	OSMIC mirrors	2005-06-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.54180

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	1.7	19.6	99.9	0.039	22.9	3.4		24541			15.98

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.79	100		0.137	7.7	3.3	3510

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3EST	1.7	19.59	24541	24499	1252	99.83	0.17	0.17	0.168	0.205	RANDOM	20.974

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
0.28			-0.08		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.553
r_dihedral_angle_4_deg	25.58
r_dihedral_angle_3_deg	11.537
r_dihedral_angle_1_deg	5.749
r_scangle_it	5.505
r_scbond_it	4.468
r_mcangle_it	3.236
r_mcbond_it	2.445
r_angle_refined_deg	1.593
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.553
r_dihedral_angle_4_deg	25.58
r_dihedral_angle_3_deg	11.537
r_dihedral_angle_1_deg	5.749
r_scangle_it	5.505
r_scbond_it	4.468
r_mcangle_it	3.236
r_mcbond_it	2.445
r_angle_refined_deg	1.593
r_nbtor_refined	0.311
r_symmetry_vdw_refined	0.249
r_symmetry_hbond_refined	0.218
r_nbd_refined	0.209
r_chiral_restr	0.13
r_xyhbond_nbd_refined	0.126
r_metal_ion_refined	0.122
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1810
Nucleic Acid Atoms
Solvent Atoms	128
Heterogen Atoms	13

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.