6G58

Structure of the alanine racemase from Staphylococcus aureus in complex with a pyridoxal 5' phosphate-derivative


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4A3Q 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2770.1 M Sodium acetate pH 4, 10 %(v/v) MPD
Crystal Properties
Matthews coefficientSolvent content
3.362.71

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.543α = 90
b = 106.767β = 90
c = 130.835γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M-F2015-09-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA0.979SLSX06SA

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
11.949.4990.13110.76.79538928.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.91.96920.451.26.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4A3Q1.949.490599478799.110.152240.151330.16971RANDOM34.78
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]
0.230.27-0.5
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.315
r_dihedral_angle_4_deg15.48
r_dihedral_angle_3_deg11.828
r_long_range_B_other6.809
r_long_range_B_refined6.808
r_dihedral_angle_1_deg5.94
r_scangle_other4.906
r_scbond_it3.234
r_scbond_other3.232
r_mcangle_other2.454
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.315
r_dihedral_angle_4_deg15.48
r_dihedral_angle_3_deg11.828
r_long_range_B_other6.809
r_long_range_B_refined6.808
r_dihedral_angle_1_deg5.94
r_scangle_other4.906
r_scbond_it3.234
r_scbond_other3.232
r_mcangle_other2.454
r_mcangle_it2.451
r_mcbond_it1.732
r_mcbond_other1.652
r_angle_refined_deg1.519
r_angle_other_deg0.933
r_chiral_restr0.09
r_bond_refined_d0.012
r_gen_planes_refined0.007
r_bond_other_d0.002
r_gen_planes_other0.002
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 Atoms6020
Nucleic Acid Atoms
Solvent Atoms482
Heterogen Atoms145

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
Cootmodel building