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Crystal structure of Microcystis aeruginosa PCC 7806 aspartate racemase in complex with DL-methyl-aspartate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5WXX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 25% (w/v) polyethylene glycol 3350, 0.2 magnesium chloride
Crystal Properties Matthews coefficient Solvent content 3.61 65.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.046 α = 90 b = 129.046 β = 90 c = 43.898 γ = 120
Symmetry Space Group P 32 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M 2017-03-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97775 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 3.4 111.76 96.1 9.1 4.8 5683
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5WXX 3.4 50 5409 274 95.98 0.18085 0.17895 0.1876 0.21735 0.2286 RANDOM 85.789
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 -1.6 5.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.075 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_4_deg 10.421 r_long_range_B_other 8.51 r_long_range_B_refined 8.509 r_dihedral_angle_1_deg 6.643 r_mcangle_it 4.75 r_mcangle_other 4.749 r_scangle_other 4.679 r_mcbond_it 2.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.075 r_dihedral_angle_3_deg 13.143 r_dihedral_angle_4_deg 10.421 r_long_range_B_other 8.51 r_long_range_B_refined 8.509 r_dihedral_angle_1_deg 6.643 r_mcangle_it 4.75 r_mcangle_other 4.749 r_scangle_other 4.679 r_mcbond_it 2.86 r_mcbond_other 2.86 r_scbond_it 2.705 r_scbond_other 2.704 r_angle_refined_deg 1.172 r_angle_other_deg 0.851 r_chiral_restr 0.058 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002 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 Atoms Number Protein Atoms 1786 Nucleic Acid Atoms Solvent Atoms 4 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing