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Crystal structure of Microcystis aeruginosa PCC 7806 aspartate racemase in complex with D-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 3.83 67.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.097 α = 90 b = 129.097 β = 90 c = 44.641 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 CCD ADSC QUANTUM 315r 2011-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.97915 SSRF BL17U
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 2.8 111.8 99.9 15.2 4.8 10736
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.85
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5WXX 2.8 42.257 10225 503 99.9 0.18421 0.18326 0.20246 0.2237 RANDOM 60.504
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 -0.59 1.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.22 r_dihedral_angle_3_deg 15.127 r_dihedral_angle_4_deg 12.988 r_long_range_B_refined 7.609 r_long_range_B_other 7.607 r_dihedral_angle_1_deg 6.663 r_scangle_other 5.229 r_mcangle_it 4.516 r_mcangle_other 4.514 r_scbond_it 3.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.22 r_dihedral_angle_3_deg 15.127 r_dihedral_angle_4_deg 12.988 r_long_range_B_refined 7.609 r_long_range_B_other 7.607 r_dihedral_angle_1_deg 6.663 r_scangle_other 5.229 r_mcangle_it 4.516 r_mcangle_other 4.514 r_scbond_it 3.117 r_scbond_other 3.116 r_mcbond_it 2.754 r_mcbond_other 2.751 r_angle_refined_deg 1.264 r_angle_other_deg 0.895 r_chiral_restr 0.069 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 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 27 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing