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Crystal structure of cytochrome domain 1 from PgcA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 289 0.3 uL protein at 10 mg per mL in 20 mM HEPES pH 7.8 100 mM NaCl, 0.28 uL Na Malonate pH 7.0 and 0.02 uL 30% W/V PEG 2000 MME
Crystal Properties Matthews coefficient Solvent content 1.66 26.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.427 α = 90 b = 68.427 β = 90 c = 27.681 γ = 90
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 2023-07-26 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 1.55 34.21 97.4 0.07 0.073 0.02 0.998 21.9 12.9 9230
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 1.55 1.58 76.8 0.512 0.543 0.173 0.915 8.6
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 1.55 34.21 1.36 9227 427 97.15 0.1568 0.1553 0.155 0.1891 0.1901
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 21.435 f_angle_d 0.997 f_chiral_restr 0.044 f_bond_d 0.009 f_plane_restr 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 433 Nucleic Acid Atoms Solvent Atoms 69 Heterogen Atoms 44
Software Software Software Name Purpose PHENIX refinement Aimless data scaling xia2 data reduction PHASER phasing