6A2F

Crystal structure of biosynthetic alanine racemase from Pseudomonas aeruginosa


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RCQ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION2934%(v/v) Tacsimate pH 4.0, 12%(w/v) polyethylene glycol 3350
Crystal Properties
Matthews coefficientSolvent content
2.8857.33

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.24α = 90
b = 78.3β = 90
c = 154.07γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2013-08-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
12.55090.40.07886.228844
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)
12.52.640.174

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 REPLACEMENTTHROUGHOUT1rcq2.550.0127388140290.450.190410.187970.23847RANDOM16.04
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]
-0.051.08-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.432
r_dihedral_angle_4_deg16.162
r_dihedral_angle_3_deg14.816
r_dihedral_angle_1_deg5.341
r_long_range_B_refined2.928
r_angle_refined_deg1.098
r_mcangle_it0.965
r_mcbond_it0.518
r_scbond_it0.467
r_chiral_restr0.067
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.432
r_dihedral_angle_4_deg16.162
r_dihedral_angle_3_deg14.816
r_dihedral_angle_1_deg5.341
r_long_range_B_refined2.928
r_angle_refined_deg1.098
r_mcangle_it0.965
r_mcbond_it0.518
r_scbond_it0.467
r_chiral_restr0.067
r_bond_refined_d0.005
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5462
Nucleic Acid Atoms
Solvent Atoms344
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing