5WXZ

Crystal structure of Microcystis aeruginosa PCC 7806 aspartate racemase in complex with D-aspartate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 5WXX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP28925% (w/v) polyethylene glycol 3350, 0.2 magnesium chloride
Crystal Properties
Matthews coefficientSolvent content
3.8367.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.097α = 90
b = 129.097β = 90
c = 44.641γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-11-12MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97915SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.8111.899.915.24.810736
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.82.85

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 REPLACEMENTTHROUGHOUT5WXX2.842.2571022550399.90.184210.183260.20246RANDOM60.504
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]
-0.59-0.3-0.591.92
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.22
r_dihedral_angle_3_deg15.127
r_dihedral_angle_4_deg12.988
r_long_range_B_refined7.609
r_long_range_B_other7.607
r_dihedral_angle_1_deg6.663
r_scangle_other5.229
r_mcangle_it4.516
r_mcangle_other4.514
r_scbond_it3.117
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.22
r_dihedral_angle_3_deg15.127
r_dihedral_angle_4_deg12.988
r_long_range_B_refined7.609
r_long_range_B_other7.607
r_dihedral_angle_1_deg6.663
r_scangle_other5.229
r_mcangle_it4.516
r_mcangle_other4.514
r_scbond_it3.117
r_scbond_other3.116
r_mcbond_it2.754
r_mcbond_other2.751
r_angle_refined_deg1.264
r_angle_other_deg0.895
r_chiral_restr0.069
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 Atoms1786
Nucleic Acid Atoms
Solvent Atoms27
Heterogen Atoms9

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing