4QAW

Structure of modular Xyn30D from Paenibacillus barcinonensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3GTNpdb entry 3GTN, 2VZP
experimental modelPDB 2VZPpdb entry 3GTN, 2VZP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829310% PEG 3350, 5% Glycerol, 0.1M Tris, Streak Seeding (2:1), pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.0659.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 174.06α = 90
b = 174.06β = 90
c = 183.932γ = 120
Symmetry
Space GroupP 32

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS 2M-F2011-10-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.440.771000.1430.04414.711.424381824371311
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.42.531000.5770.1782.611.5

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 3GTN, 2VZP2.440.772437132315611215199.980.194170.193730.20246RANDOM12.621
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]
-0.26-0.260.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.972
r_dihedral_angle_4_deg23.512
r_dihedral_angle_3_deg14.498
r_dihedral_angle_1_deg6.903
r_long_range_B_refined2.503
r_long_range_B_other2.502
r_mcangle_other1.542
r_mcangle_it1.192
r_angle_refined_deg1.18
r_scangle_other1.176
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.972
r_dihedral_angle_4_deg23.512
r_dihedral_angle_3_deg14.498
r_dihedral_angle_1_deg6.903
r_long_range_B_refined2.503
r_long_range_B_other2.502
r_mcangle_other1.542
r_mcangle_it1.192
r_angle_refined_deg1.18
r_scangle_other1.176
r_angle_other_deg0.762
r_scbond_other0.679
r_mcbond_it0.648
r_mcbond_other0.648
r_scbond_it0.402
r_chiral_restr0.072
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms33155
Nucleic Acid Atoms
Solvent Atoms95
Heterogen Atoms16

Software

Software
Software NamePurpose
MxCuBEdata collection
MOLREPphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling