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Crystal structure of Heme-Oxygenase from Corynebacterium diphtheriae complexed with Cobalt-porphyrine (HumO-Co(III))
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 3.5 294 2-16% PEG 1000 and 0.1M citric acid at pH 3.5
Crystal Properties Matthews coefficient Solvent content 2.27 45.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.715 α = 90 b = 70.264 β = 90 c = 95.223 γ = 90
Symmetry Space Group C 2 2 21
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 9M 2023-04-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID30B 0.87313 ESRF ID30B
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 1.15 48 97.6 0.086 0.998 8.3 5.6 76745 1 13.17
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.15 1.17 83.9 0.485 1 4.7
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 1.15 48 1.33 76634 4007 97.4 0.1451 0.1433 0.1433 0.1796 0.1797 21.71
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 12.9351 f_angle_d 1.4709 f_chiral_restr 0.0699 f_plane_restr 0.0075 f_bond_d 0.0065
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1669 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 67
Software Software Software Name Purpose PHENIX refinement XDS data reduction Aimless data scaling PHASER phasing