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Crystal structure of the Zn-directed tetramer of the engineered cyt cb 562 variant, C96V AB5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3IQ5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 36% Polypropylene glycol (P400), 100 mM bis-tris, 200 mM magnessium chloride
Crystal Properties Matthews coefficient Solvent content 2.21 44.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.757 α = 90 b = 53.757 β = 90 c = 250.721 γ = 120
Symmetry Space Group P 61 2 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 2018-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 11C 0.979 PAL/PLS 11C
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 46.55 99.98 0.576 24.22 30.2 15537
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.05 2.1 1.186
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 3IQ5 2 46.55 14737 796 99.99 0.1818 0.1787 0.1873 0.2398 0.2413 RANDOM 24.374
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] 0.01 0.01 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.146 r_dihedral_angle_3_deg 14.72 r_dihedral_angle_4_deg 8.552 r_dihedral_angle_1_deg 5.673 r_angle_refined_deg 1.607 r_angle_other_deg 1.408 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.146 r_dihedral_angle_3_deg 14.72 r_dihedral_angle_4_deg 8.552 r_dihedral_angle_1_deg 5.673 r_angle_refined_deg 1.607 r_angle_other_deg 1.408 r_chiral_restr 0.078 r_bond_refined_d 0.013 r_gen_planes_refined 0.009 r_gen_planes_other 0.007 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1656 Nucleic Acid Atoms Solvent Atoms 258 Heterogen Atoms 94
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling MOLREP phasing PDB_EXTRACT data extraction