☰ Navigation Tabs
Structure of ClpP from Staphylococcus aureus in complex with ZY7
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ST6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 289 0.1 M Sodium chloride, 0.1 M BICINE pH9.0, 20% PEG monomethyl ether 550
Crystal Properties Matthews coefficient Solvent content 2.61 52.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.368 α = 90 b = 174.507 β = 90 c = 194.455 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 EIGER X 16M 2018-06-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.988 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 2.74 129.88 92.4 0.079 0.088 0.039 0.993 11.8 4 62269
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.75 2.85 82.2 0.273 0.336 0.19 0.566 2.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.74 129.88 62269 3410 75.79 0.22678 0.22558 0.2257 0.24868 0.2479 RANDOM 49.868
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] 2.14 1.87 -4.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.197 r_dihedral_angle_4_deg 20.881 r_dihedral_angle_3_deg 19.007 r_long_range_B_refined 7.205 r_long_range_B_other 7.204 r_dihedral_angle_1_deg 5.838 r_scangle_other 5.166 r_mcangle_it 4.756 r_mcangle_other 4.756 r_scbond_it 3.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.197 r_dihedral_angle_4_deg 20.881 r_dihedral_angle_3_deg 19.007 r_long_range_B_refined 7.205 r_long_range_B_other 7.204 r_dihedral_angle_1_deg 5.838 r_scangle_other 5.166 r_mcangle_it 4.756 r_mcangle_other 4.756 r_scbond_it 3.103 r_scbond_other 3.102 r_mcbond_it 2.936 r_mcbond_other 2.934 r_angle_refined_deg 1.644 r_angle_other_deg 1.482 r_chiral_restr 0.086 r_bond_refined_d 0.011 r_bond_other_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.005 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 20112 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 518
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling autoPROC data reduction PHASER phasing