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Crystal structure of cytochrome domain 3 from PgcA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 1:1 mixture of 20 mg per mL protein in 20 mM HEPES 100 mM NaCl pH 7.8 with 2.3 M Na Malonate pH 7.0, 1.8% Jeffamine ED-2001
Crystal Properties Matthews coefficient Solvent content 1.8 31.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.564 α = 90 b = 55.033 β = 99.3 c = 37.456 γ = 90
Symmetry Space Group C 1 2 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 EIGER2 XE 16M 2023-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 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 1.9 44.28 99.8 0.135 0.147 0.056 0.996 8.2 6.8 12027
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 1.9 1.94 97.9 0.631 0.702 0.301 0.842 5.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1.9 44.28 1.34 11995 599 99.57 0.2232 0.221 0.2209 0.2632 0.2626
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 16.745 f_angle_d 1.096 f_chiral_restr 0.057 f_plane_restr 0.016 f_bond_d 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1028 Nucleic Acid Atoms Solvent Atoms 179 Heterogen Atoms 96
Software Software Software Name Purpose PHENIX refinement Aimless data scaling xia2 data reduction PHASER phasing