5XNK

Crystal structure of Microcystis aeruginosa PCC 7806 aspartate racemase in complex with DL-methyl-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
3.6165.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 129.046α = 90
b = 129.046β = 90
c = 43.898γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-03-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL19U10.97775SSRFBL19U1

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
13.4111.7696.19.14.85683

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 REPLACEMENTTHROUGHOUT5WXX3.450540927495.980.180850.178950.21735RANDOM85.789
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]
-1.6-0.8-1.65.19
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.075
r_dihedral_angle_3_deg13.143
r_dihedral_angle_4_deg10.421
r_long_range_B_other8.51
r_long_range_B_refined8.509
r_dihedral_angle_1_deg6.643
r_mcangle_it4.75
r_mcangle_other4.749
r_scangle_other4.679
r_mcbond_it2.86
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.075
r_dihedral_angle_3_deg13.143
r_dihedral_angle_4_deg10.421
r_long_range_B_other8.51
r_long_range_B_refined8.509
r_dihedral_angle_1_deg6.643
r_mcangle_it4.75
r_mcangle_other4.749
r_scangle_other4.679
r_mcbond_it2.86
r_mcbond_other2.86
r_scbond_it2.705
r_scbond_other2.704
r_angle_refined_deg1.172
r_angle_other_deg0.851
r_chiral_restr0.058
r_bond_refined_d0.007
r_gen_planes_refined0.005
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 Atoms1786
Nucleic Acid Atoms
Solvent Atoms4
Heterogen Atoms20

Software

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