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Bdellovibrio bacteriovorus PGI in P1211 spacegroup
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NSS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 291 0.2 M ammonium acetate
0.1 M sodium acetate pH4.0
15% w/v PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.59 52.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.92 α = 90 b = 118.1 β = 118.41 c = 138.98 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 PIXEL DECTRIS PILATUS 6M-F 2016-06-08 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 Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.74 59.54 98.8 0.09 0.116 0.073 0.982 8.7 3.9 395364
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.77 0.607 0.788 0.495 0.615 1.5
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 7NSS 1.74 59.54 375276 20056 98.74 0.2238 0.2223 0.22 0.2528 0.2486 RANDOM 21.168
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] 0.37 0.05 -1.37 0.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.796 r_dihedral_angle_4_deg 14.101 r_dihedral_angle_3_deg 13.402 r_dihedral_angle_1_deg 6.214 r_angle_other_deg 2.243 r_angle_refined_deg 1.341 r_chiral_restr 0.071 r_bond_other_d 0.035 r_gen_planes_other 0.009 r_bond_refined_d 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.796 r_dihedral_angle_4_deg 14.101 r_dihedral_angle_3_deg 13.402 r_dihedral_angle_1_deg 6.214 r_angle_other_deg 2.243 r_angle_refined_deg 1.341 r_chiral_restr 0.071 r_bond_other_d 0.035 r_gen_planes_other 0.009 r_bond_refined_d 0.007 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 25476 Nucleic Acid Atoms Solvent Atoms 3254 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction xia2 data reduction xia2 data scaling PHENIX phasing