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ZmpB metallopeptidase in complex with an O-glycopeptide (a2,6-sialylated core-3 pentapeptide).
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 3.2 61.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.18 α = 90 b = 68.95 β = 90 c = 171.57 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 MARMOSAIC 325 mm CCD 2011-07-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.9790 SSRL BL9-2
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 1.6 40 96 0.054 20.9 7.2 99964
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 1.6 1.69 76 0.354 4.6 5.7
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 1.6 40 94972 4992 95.86 0.1595 0.15814 0.159 0.1855 0.1866 RANDOM 22.982
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] -0.51 1.91 -1.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.396 r_dihedral_angle_4_deg 18.901 r_dihedral_angle_3_deg 12.678 r_long_range_B_refined 6.795 r_dihedral_angle_1_deg 6.158 r_scbond_it 2.74 r_mcangle_it 2.437 r_angle_refined_deg 1.657 r_mcbond_it 1.602 r_chiral_restr 0.118
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.396 r_dihedral_angle_4_deg 18.901 r_dihedral_angle_3_deg 12.678 r_long_range_B_refined 6.795 r_dihedral_angle_1_deg 6.158 r_scbond_it 2.74 r_mcangle_it 2.437 r_angle_refined_deg 1.657 r_mcbond_it 1.602 r_chiral_restr 0.118 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4169 Nucleic Acid Atoms Solvent Atoms 794 Heterogen Atoms 46
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling MOLREP phasing