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Crystal structure of the basic protease BprV from the ovine footrot pathogen, Dichelobacter nodosus
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 293 PEG 3350, pH 6.5, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.04 39.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.497 α = 90 b = 89.637 β = 113.61 c = 47.654 γ = 90
Symmetry Space Group P 1 21 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 mirrors M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R 1.542
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 44.81 20048 20018
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 27.724 20018 1022 99.82 0.166 0.1627 0.1652 0.2255 0.2199 RANDOM 16.1343
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] -0.98 -0.12 -0.93 1.81
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.065 r_dihedral_angle_4_deg 21.623 r_dihedral_angle_3_deg 13.598 r_dihedral_angle_1_deg 5.583 r_scangle_it 4.185 r_scbond_it 3.113 r_mcangle_it 1.6 r_angle_refined_deg 1.153 r_mcbond_it 0.825 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.065 r_dihedral_angle_4_deg 21.623 r_dihedral_angle_3_deg 13.598 r_dihedral_angle_1_deg 5.583 r_scangle_it 4.185 r_scbond_it 3.113 r_mcangle_it 1.6 r_angle_refined_deg 1.153 r_mcbond_it 0.825 r_nbtor_refined 0.297 r_nbd_refined 0.198 r_metal_ion_refined 0.163 r_symmetry_vdw_refined 0.156 r_symmetry_hbond_refined 0.137 r_xyhbond_nbd_refined 0.126 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2488 Nucleic Acid Atoms Solvent Atoms 312 Heterogen Atoms 3
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection