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Bd3459 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 5CEA 5CEA & 5CEB experimental model PDB 5CEB 5CEA & 5CEB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 298 0.1M citrate pH 5.0, 3.2M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 1.98 38.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.61 α = 90 b = 59.17 β = 90 c = 192.27 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 PIXEL DECTRIS PILATUS 6M-F 2014-08-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 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 1.36 100 97.2 0.032 23.4 6 117291
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 5CEA & 5CEB 1.36 96.14 117290 6194 96.99 0.1426 0.1412 0.1688 0.1871 RANDOM 23.69
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] -0.81 1.19 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.554 r_sphericity_free 25.144 r_dihedral_angle_4_deg 11.376 r_dihedral_angle_3_deg 11.261 r_sphericity_bonded 10.846 r_dihedral_angle_1_deg 5.579 r_mcangle_it 1.87 r_rigid_bond_restr 1.744 r_angle_refined_deg 1.442 r_mcbond_it 1.389
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.554 r_sphericity_free 25.144 r_dihedral_angle_4_deg 11.376 r_dihedral_angle_3_deg 11.261 r_sphericity_bonded 10.846 r_dihedral_angle_1_deg 5.579 r_mcangle_it 1.87 r_rigid_bond_restr 1.744 r_angle_refined_deg 1.442 r_mcbond_it 1.389 r_mcbond_other 1.389 r_angle_other_deg 0.923 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4549 Nucleic Acid Atoms Solvent Atoms 493 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing