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Bd0816 Predatory Endopeptidase from Bdellovibrio bacteriovorus in complex with immunity protein Bd3460
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CEC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 298 0.1M Na HEPES pH 7.5, 0.2M MgCl2, 25% w/v PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.63 53.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 237.45 α = 90 b = 212.32 β = 90 c = 90.9 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS 6M-F 2014-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.92001 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.48 100 99 0.156 15.1 13.5 153169
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 5CEC 2.48 100 153169 7978 98.79 0.2167 0.215 0.2491 0.2345 RANDOM 43.935
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] 2.18 -0.49 -1.69
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.435 r_dihedral_angle_3_deg 16.141 r_dihedral_angle_4_deg 13.982 r_dihedral_angle_1_deg 6.437 r_angle_other_deg 1.861 r_mcangle_it 1.819 r_angle_refined_deg 1.683 r_mcbond_it 1.117 r_mcbond_other 1.117 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.435 r_dihedral_angle_3_deg 16.141 r_dihedral_angle_4_deg 13.982 r_dihedral_angle_1_deg 6.437 r_angle_other_deg 1.861 r_mcangle_it 1.819 r_angle_refined_deg 1.683 r_mcbond_it 1.117 r_mcbond_other 1.117 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_bond_other_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 27359 Nucleic Acid Atoms Solvent Atoms 1356 Heterogen Atoms 4
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing