Experiment: 2BD4

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 LYS-SER (50MG/ML) IN 250MM SODIUM ACETATE (PH 5.0) (5 MICROLITRES) FOR 60 MIN, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.03	39.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.227	α = 90
b = 57.935	β = 90
c = 74.774	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	2005-06-17	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	15.7	99.9	0.043	20.6	3.5		24646			15.4

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)
	1.7	1.79	100		0.13	8.6	3.4	3558

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	15.7	24646	24599	1254	99.83	0.188	0.188	0.186	0.22	RANDOM	19.622

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]
0.1			0.08		-0.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.887
r_dihedral_angle_4_deg	25.077
r_dihedral_angle_3_deg	12.087
r_dihedral_angle_1_deg	6.061
r_scangle_it	3.687
r_scbond_it	2.735
r_mcangle_it	1.82
r_angle_refined_deg	1.717
r_mcbond_it	1.226
r_nbtor_refined	0.312

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.887
r_dihedral_angle_4_deg	25.077
r_dihedral_angle_3_deg	12.087
r_dihedral_angle_1_deg	6.061
r_scangle_it	3.687
r_scbond_it	2.735
r_mcangle_it	1.82
r_angle_refined_deg	1.717
r_mcbond_it	1.226
r_nbtor_refined	0.312
r_symmetry_vdw_refined	0.25
r_nbd_refined	0.219
r_symmetry_hbond_refined	0.2
r_chiral_restr	0.139
r_metal_ion_refined	0.13
r_xyhbond_nbd_refined	0.126
r_bond_refined_d	0.019
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1810
Nucleic Acid Atoms
Solvent Atoms	100
Heterogen Atoms	11

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.