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Structure of coproheme-LmCpfC
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HK6
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 0.1 M BIS-TRIS pH 5.5, 25% PEG3350, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.21 44.34
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.47 α = 90 b = 68.14 β = 103.06 c = 62.91 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 EIGER X 16M 2019-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 Diamond I03
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 1.64 36.51 99.04 0.04989 0.07055 0.04989 0.997 12.36 1.9 37446 24.29
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 1.64 1.699 96.68 0.607 0.8584 0.607 0.561 1.15 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 2HK6 1.64000868883 36.5007995703 1.34351924443 37444 1822 99.047719818 0.172783391952 0.171330289619 0.1759 0.201404057491 0.2066 25.8354837015
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 4.6899750646 f_angle_d 0.912247197836 f_chiral_restr 0.0585727243746 f_bond_d 0.0088695411418 f_plane_restr 0.00707296520445
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2500 Nucleic Acid Atoms Solvent Atoms 323 Heterogen Atoms 61
Software Software Software Name Purpose PHENIX refinement PHENIX refinement XDS data reduction XDS data scaling PHASER phasing