6G56

Apo-structure of the alanine racemase from Staphylococcus aureus


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP2772M Ammonium sulphate, 50mM Sodium acetate, pH 6
Crystal Properties
Matthews coefficientSolvent content
2.5852.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.701α = 90
b = 114.521β = 90
c = 126.093γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2015-04-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.976ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.1584.781000.1660.20.9965.25145834.4
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.152.2991.730.850.45.1

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 REPLACEMENTTHROUGHOUT4A3Q2.1584.7848216253898.10.218710.216850.25386RANDOM33.99
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]
-0.61.12-0.52
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.492
r_dihedral_angle_4_deg17.648
r_dihedral_angle_3_deg12.904
r_long_range_B_refined7.793
r_long_range_B_other7.787
r_dihedral_angle_1_deg6.392
r_scangle_other5.704
r_scbond_it4.241
r_scbond_other4.235
r_mcangle_it3.271
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.492
r_dihedral_angle_4_deg17.648
r_dihedral_angle_3_deg12.904
r_long_range_B_refined7.793
r_long_range_B_other7.787
r_dihedral_angle_1_deg6.392
r_scangle_other5.704
r_scbond_it4.241
r_scbond_other4.235
r_mcangle_it3.271
r_mcangle_other3.271
r_mcbond_it2.161
r_mcbond_other2.16
r_angle_refined_deg1.428
r_angle_other_deg0.94
r_chiral_restr0.081
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_bond_other_d0.002
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 Atoms6000
Nucleic Acid Atoms
Solvent Atoms297
Heterogen Atoms138

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
PHASERphasing
Cootmodel building