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Crystal structure of the HmuO, heme oxygenase from Corynebacterium diphtheriae, in complex with azide-bound verdoheme
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 5.4 303 50mM MES (pH 5.4), 2.4M ammonium sulfate, 0.27M sodium bromide, 0.1 % (v/v) dioxane, VAPOR DIFFUSION, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.1 41.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.609 α = 90 b = 63.649 β = 130.34 c = 78.52 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 CCD ADSC QUANTUM 270 2008-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 1.0 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym I (Observed) 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 1.7 50 96.2 0.056 23.6 4.36 37613
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.7 2 82.8 0.289 2.84
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1IW0 1.71 50 35684 4159 95.77 0.18188 0.17839 0.1777 0.21283 0.2118 RANDOM
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] -0.46 0.02 -1.29 1.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.035 r_dihedral_angle_3_deg 15.023 r_dihedral_angle_4_deg 14.425 r_dihedral_angle_1_deg 4.843 r_scangle_it 3.526 r_angle_refined_deg 2.469 r_scbond_it 1.946 r_mcangle_it 1.384 r_mcbond_it 0.815 r_chiral_restr 0.335
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.035 r_dihedral_angle_3_deg 15.023 r_dihedral_angle_4_deg 14.425 r_dihedral_angle_1_deg 4.843 r_scangle_it 3.526 r_angle_refined_deg 2.469 r_scbond_it 1.946 r_mcangle_it 1.384 r_mcbond_it 0.815 r_chiral_restr 0.335 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.22 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.183 r_xyhbond_nbd_refined 0.149 r_metal_ion_refined 0.104 r_bond_refined_d 0.013 r_gen_planes_refined 0.01 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3312 Nucleic Acid Atoms Solvent Atoms 310 Heterogen Atoms 188
Software Software Software Name Purpose REFMAC refinement