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Crystal structure of the autoprocessed Vibriolysin MCP-02 with E369A mutation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3NQX PDB ENTRY 3NQX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 9% PEG 10000, Tris buffer, 0.01M NiCl2 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.82 56.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.535 α = 90 b = 82.535 β = 90 c = 154.206 γ = 120
Symmetry Space Group P 32 2 1
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++ 2009-02-06 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E+ DW 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 2.05 16.97 100 0.073 20 8.6 36839 36839 37
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 2.05 2.1 100 0.453 30 16.5 36800
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 3NQX 2.05 16.97 36839 1941 99.91 0.18105 0.17896 0.1824 0.21991 0.2183 RANDOM 20.197
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] 0.04 0.02 0.04 -0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.283 r_dihedral_angle_4_deg 18.227 r_dihedral_angle_3_deg 15.14 r_dihedral_angle_1_deg 9.233 r_scangle_it 3.043 r_scbond_it 2.208 r_angle_refined_deg 1.613 r_mcangle_it 1.458 r_mcbond_it 0.89 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.283 r_dihedral_angle_4_deg 18.227 r_dihedral_angle_3_deg 15.14 r_dihedral_angle_1_deg 9.233 r_scangle_it 3.043 r_scbond_it 2.208 r_angle_refined_deg 1.613 r_mcangle_it 1.458 r_mcbond_it 0.89 r_nbtor_refined 0.303 r_nbd_refined 0.219 r_symmetry_vdw_refined 0.203 r_chiral_restr 0.178 r_xyhbond_nbd_refined 0.145 r_symmetry_hbond_refined 0.125 r_metal_ion_refined 0.024 r_bond_refined_d 0.016 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 3678 Nucleic Acid Atoms Solvent Atoms 382 Heterogen Atoms 2
Software Software Software Name Purpose CrystalClear data collection AMoRE phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling