☰ Navigation Tabs
Crystal structure of Microcystis aeruginosa PCC 7806 aspartate/glutamate racemase in complex with D-glutamate
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 3.62 66.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.304 α = 90 b = 129.304 β = 90 c = 43.811 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 2017-04-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.97776 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 3.22 111.98 100 21.7 8.4 7030
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 3.22 50 6704 309 99.84 0.18966 0.18739 0.1891 0.24088 0.2346 RANDOM 82.556
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] -1.73 -0.86 -1.73 5.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.814 r_dihedral_angle_3_deg 13.862 r_long_range_B_refined 7.204 r_long_range_B_other 7.204 r_dihedral_angle_1_deg 6.615 r_scangle_other 4.899 r_mcangle_other 4.288 r_mcangle_it 4.285 r_scbond_it 2.868 r_scbond_other 2.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.814 r_dihedral_angle_3_deg 13.862 r_long_range_B_refined 7.204 r_long_range_B_other 7.204 r_dihedral_angle_1_deg 6.615 r_scangle_other 4.899 r_mcangle_other 4.288 r_mcangle_it 4.285 r_scbond_it 2.868 r_scbond_other 2.851 r_mcbond_it 2.606 r_mcbond_other 2.592 r_dihedral_angle_4_deg 2.544 r_angle_refined_deg 1.184 r_angle_other_deg 0.866 r_chiral_restr 0.063 r_bond_refined_d 0.007 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001 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 Atoms Number Protein Atoms 1786 Nucleic Acid Atoms Solvent Atoms 8 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing