☰ Navigation Tabs
ZmpB metallopeptidase from Clostridium perfringens
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5KDJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 PEG 3350, Na/K tartrate, HEPES pH 7.5
Crystal Properties Matthews coefficient Solvent content 3.19 61.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.89 α = 90 b = 68.02 β = 90 c = 170.86 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 CCD RAYONIX MX300HE 2015-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08B1-1 0.97950 CLSI 08B1-1
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 1.66 43.09 99.9 0.054 18.5 7.2 92133
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.66 1.68 100 0.249 5.3 6.6
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 5KDJ 1.66 43.09 87452 4594 99.89 0.15508 0.15376 0.1666 0.18046 0.1904 RANDOM 22.8
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] -1.36 2.9 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.886 r_dihedral_angle_4_deg 20.301 r_dihedral_angle_3_deg 13.113 r_dihedral_angle_1_deg 6.402 r_long_range_B_refined 6.282 r_long_range_B_other 6.281 r_scangle_other 4.569 r_scbond_it 3.02 r_scbond_other 3.017 r_mcangle_other 2.613
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.886 r_dihedral_angle_4_deg 20.301 r_dihedral_angle_3_deg 13.113 r_dihedral_angle_1_deg 6.402 r_long_range_B_refined 6.282 r_long_range_B_other 6.281 r_scangle_other 4.569 r_scbond_it 3.02 r_scbond_other 3.017 r_mcangle_other 2.613 r_mcangle_it 2.612 r_angle_refined_deg 1.863 r_mcbond_it 1.78 r_mcbond_other 1.776 r_angle_other_deg 0.898 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 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 4063 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing