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Crystal structure of the heme oxygenase from Corynebacterium diphtheriae (HmuO) in complex with heme binding ditiothreitol (DTT)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1IW0 PDB ENTRY 1IW0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.1 303 2.2M (NH4)2SO4, 50mM MES (pH6.1), 0.1% Dioxane, 0.25M Sodium Iodide with 50mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 303K
Crystal Properties Matthews coefficient Solvent content 2.48 50.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.117 α = 90 b = 62.563 β = 100.67 c = 108.002 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 90 CCD ADSC QUANTUM 210 2004-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1 Photon Factory AR-NW12A
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 1.5 50 98 0.05 45.5 7 113340 111073 1
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) 1.5 1.55 90.1 0.378 2.62 6.3 10120
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 PDB ENTRY 1IW0 1.5 30 99940 11109 98.03 0.19698 0.19399 0.2 0.22351 0.2274 RANDOM 25.139
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] -0.38 0.37 1.38 -0.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.72 r_dihedral_angle_4_deg 19.162 r_dihedral_angle_3_deg 14.875 r_scangle_it 5.639 r_dihedral_angle_1_deg 5.169 r_scbond_it 3.732 r_angle_refined_deg 2.519 r_mcangle_it 2.351 r_mcbond_it 1.494 r_chiral_restr 0.181
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.72 r_dihedral_angle_4_deg 19.162 r_dihedral_angle_3_deg 14.875 r_scangle_it 5.639 r_dihedral_angle_1_deg 5.169 r_scbond_it 3.732 r_angle_refined_deg 2.519 r_mcangle_it 2.351 r_mcbond_it 1.494 r_chiral_restr 0.181 r_bond_refined_d 0.03 r_gen_planes_refined 0.015 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 4957 Nucleic Acid Atoms Solvent Atoms 484 Heterogen Atoms 198
Software Software Software Name Purpose CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing