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Crystal structure of rat heme oxygenase-1 in complex with ferrous verdoheme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UBB PDB ENTRY 1UBB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 4.0M sodium formate, 10mM sodium azide, pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.42 49.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.346 α = 90 b = 65.346 β = 90 c = 120.24 γ = 120
Symmetry Space Group P 32 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 RIGAKU JUPITER 210 2008-06-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL38B1 1.0 SPring-8 BL38B1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.2 50 98.9 0.068 12.5 4.9 15541 15371
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.28 90.7 0.342 2.9 3.7 1396
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 1UBB 2.2 32.67 15541 14728 775 98.94 0.19185 0.18941 0.1931 0.24005 0.2429 RANDOM 35.809
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] 0.31 0.15 0.31 -0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.595 r_dihedral_angle_3_deg 16.034 r_dihedral_angle_4_deg 15.593 r_dihedral_angle_1_deg 5.242 r_scangle_it 2.841 r_scbond_it 1.835 r_angle_refined_deg 1.792 r_mcangle_it 1.182 r_mcbond_it 0.75 r_nbtor_refined 0.305
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.595 r_dihedral_angle_3_deg 16.034 r_dihedral_angle_4_deg 15.593 r_dihedral_angle_1_deg 5.242 r_scangle_it 2.841 r_scbond_it 1.835 r_angle_refined_deg 1.792 r_mcangle_it 1.182 r_mcbond_it 0.75 r_nbtor_refined 0.305 r_symmetry_hbond_refined 0.223 r_symmetry_vdw_refined 0.212 r_nbd_refined 0.207 r_xyhbond_nbd_refined 0.16 r_chiral_restr 0.091 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 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_refined 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 1723 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing