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Crystal structure of a ParB E93A mutant from Myxococcus xanthus bound to CDP and monothiophosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7BNK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 294 0.1 M Phosphate-citrate pH 4.2; 40% (v/v) PEG 300
Crystal Properties Matthews coefficient Solvent content 2.78 55.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.12 α = 90 b = 80.37 β = 90 c = 136.83 γ = 90
Symmetry Space Group P 21 21 21
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 PILATUS3 6M 2021-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.97625 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.89 41.99 99.7 0.093 14.18 12.3 39707 39.42
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 1.95 1.938 0.578 1.09
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 7BNK 1.89 41.99 37721 1986 99.6 0.197 0.196 0.2068 0.216 0.214 RANDOM 61.86
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] -2.55 -1.91 4.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.072 r_dihedral_angle_4_deg 17.945 r_dihedral_angle_3_deg 15.138 r_dihedral_angle_1_deg 5.291 r_angle_refined_deg 1.319 r_angle_other_deg 1.132 r_chiral_restr 0.123 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.072 r_dihedral_angle_4_deg 17.945 r_dihedral_angle_3_deg 15.138 r_dihedral_angle_1_deg 5.291 r_angle_refined_deg 1.319 r_angle_other_deg 1.132 r_chiral_restr 0.123 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3052 Nucleic Acid Atoms Solvent Atoms 60 Heterogen Atoms 81
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PHASER phasing XDS data reduction