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Bd3459 Predatory Endopeptidase from Bdellovibrio bacteriovorus, K38M form
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V39
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1M potassium thiocyanate, 30% w/v PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 2.43 49.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.93 α = 63.89 b = 65.04 β = 83.27 c = 73.816 γ = 83.2
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 2014-11-30 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.91739 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 1.93 100 85.7 0.036 16.2 3.8 56655
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 3v39 1.93 66.11 56655 2881 85.61 0.1976 0.1958 0.2025 0.2322 0.2369 RANDOM 44.292
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] 1.86 1.28 -0.85 0.56 -0.17 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.398 r_dihedral_angle_4_deg 18.64 r_dihedral_angle_3_deg 13.898 r_dihedral_angle_1_deg 6.6 r_mcangle_it 3.579 r_mcbond_it 2.616 r_mcbond_other 2.615 r_angle_refined_deg 1.629 r_angle_other_deg 1.178 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.398 r_dihedral_angle_4_deg 18.64 r_dihedral_angle_3_deg 13.898 r_dihedral_angle_1_deg 6.6 r_mcangle_it 3.579 r_mcbond_it 2.616 r_mcbond_other 2.615 r_angle_refined_deg 1.629 r_angle_other_deg 1.178 r_chiral_restr 0.103 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5971 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction XDS data reduction XSCALE data scaling PHASER phasing