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1.93 Angstrom Resolution Crystal Structure of Peptidase M23 from Neisseria gonorrhoeae.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3SLU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 292 Protein: 13.0 mg/ml, 0.5M Sodium chloride, 0.01M Tris-HCl pH 8.3;
Screen: Classics II (C2), 1.1M Ammonium tartrate pH 7.0;
Cryo: 4M Sodium formate.
Crystal Properties Matthews coefficient Solvent content 2.26 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.964 α = 90 b = 66.964 β = 90 c = 181.584 γ = 90
Symmetry Space Group P 43 21 2
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 MARMOSAIC 300 mm CCD C(111) 2018-08-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-F 0.97872 APS 21-ID-F
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) Rpim I (All) 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 1.93 30 100 0.049 0.049 0.053 0.02 38.7 7.2 32097 -3 36.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.93 1.96 100 0.841 0.841 0.904 0.33 0.864 2.5 7.3
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 3SLU 1.93 29.95 30417 1606 99.95 0.19079 0.18849 0.1959 0.23554 0.239 RANDOM 44.127
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] 1.52 1.52 -3.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.818 r_dihedral_angle_4_deg 12.608 r_dihedral_angle_3_deg 11.056 r_long_range_B_refined 7.113 r_long_range_B_other 7.098 r_dihedral_angle_1_deg 3.78 r_scangle_other 3.566 r_mcangle_it 2.887 r_mcangle_other 2.887 r_scbond_it 2.239
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.818 r_dihedral_angle_4_deg 12.608 r_dihedral_angle_3_deg 11.056 r_long_range_B_refined 7.113 r_long_range_B_other 7.098 r_dihedral_angle_1_deg 3.78 r_scangle_other 3.566 r_mcangle_it 2.887 r_mcangle_other 2.887 r_scbond_it 2.239 r_scbond_other 2.235 r_mcbond_it 1.863 r_mcbond_other 1.859 r_angle_refined_deg 1.388 r_angle_other_deg 0.408 r_chiral_restr 0.056 r_gen_planes_refined 0.053 r_gen_planes_other 0.047 r_bond_refined_d 0.008 r_bond_other_d 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 2760 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing