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Crystal structure of Heme-Oxygenase mutant H20C 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 5.5 294 17% PEG10000, 100 mM BIS-TRIS pH 5.5, 100 mM ammonium acetate
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.744 α = 90 b = 69.331 β = 109.62 c = 63.177 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 9M 2024-04-24 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) 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 2.3 45.16 98.9 0.18 0.093 0.991 6.5 3.8 15723 1 34.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 98.1 1.183 0.62 0.534 1.5 3.7
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 2.3 45.16 1.33 15702 765 98.63 0.23 0.227 0.2266 0.2843 0.2836
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 16.41 f_angle_d 1.395 f_chiral_restr 0.035 f_bond_d 0.005 f_plane_restr 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3318 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 86
Software Software Software Name Purpose PHENIX refinement Aimless data scaling XDS data reduction PHASER phasing