5I4M

Crystal structure of Amidase, hydantoinase/carbamoylase family from Burkholderia vietnamiensis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4WJB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.5290MCSG1 screen B10: 24% PEG 4000, 20% glycerol, 160mM MgCl2, 100mM Tris/HCl pH 8.5; BuviA.12245.b.B2.PS02523 at 18.3 mg/ml, + 3mM Alanine; cryo: direct; tray 267436b10, puck LWQ9-7
Crystal Properties
Matthews coefficientSolvent content
2.3948.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.46α = 90
b = 124.23β = 101.94
c = 77.04γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-2252015-12-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-F0.97872APS21-ID-F

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)CC (Half)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
11.847.93599.90.0920.99612.333.880654-313.18
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8599.90.5162.59

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4wjb1.847.9351.3580600195999.910.13930.13850.171216.793
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]
RMS Deviations
KeyRefinement Restraint Deviation
f_dihedral_angle_d15.678
f_angle_d0.812
f_chiral_restr0.054
f_plane_restr0.006
f_bond_d0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6166
Nucleic Acid Atoms
Solvent Atoms1026
Heterogen Atoms26

Software

Software
Software NamePurpose
XDSdata reduction
XSCALEdata scaling
MOLREPphasing
Cootmodel building
PHENIXrefinement
PDB_EXTRACTdata extraction