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Crystal structure of vibriolysin MCP-02 mature enzyme, a zinc metalloprotease from M4 family
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EZM PDB ENTRY 1EZM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 12% PEG 3000, 0.1M Bis-Tris, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.801 α = 90 b = 73.792 β = 90 c = 91.421 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 IMAGE PLATE RIGAKU RAXIS IV++ 2008-12-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ SUPERBRIGHT 1.48
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 1.7 21.45 100 0.185 54 3.4 32935 32935
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 1.7 1.76 100 0.18 9 3.2 32935
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 PDB ENTRY 1EZM 1.7 21.45 31266 1669 98.74 0.17649 0.17433 0.1715 0.21739 0.2107 RANDOM 16.182
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.131 r_dihedral_angle_4_deg 16.336 r_dihedral_angle_3_deg 14.274 r_dihedral_angle_1_deg 6.176 r_scangle_it 3.412 r_scbond_it 2.532 r_angle_refined_deg 1.608 r_mcangle_it 1.361 r_mcbond_it 0.818 r_symmetry_vdw_refined 0.336
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.131 r_dihedral_angle_4_deg 16.336 r_dihedral_angle_3_deg 14.274 r_dihedral_angle_1_deg 6.176 r_scangle_it 3.412 r_scbond_it 2.532 r_angle_refined_deg 1.608 r_mcangle_it 1.361 r_mcbond_it 0.818 r_symmetry_vdw_refined 0.336 r_nbtor_refined 0.311 r_nbd_refined 0.263 r_xyhbond_nbd_refined 0.229 r_chiral_restr 0.171 r_symmetry_hbond_refined 0.152 r_metal_ion_refined 0.044 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2277 Nucleic Acid Atoms Solvent Atoms 437 Heterogen Atoms 2
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling