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Crystal structure of human heme oxygenase 1 H25R with biliverdin bound
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.4 293 100mM HEPES
2.1M Ammonium sulfate
0.9% 1,6-hexanediol
Crystal Properties Matthews coefficient Solvent content 2.21 44.35
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.7 α = 90 b = 54.74 β = 99.37 c = 72.51 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 CCD ADSC QUANTUM 315 2014-11-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
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 2.08 43.5 93.3 0.079 14.4 5.1 26949
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) 1 2.08 2.19 75.3 0.407 3.5 4.4
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 1N45 2.08 43.5 25550 1399 93.17 0.18503 0.18269 0.1901 0.22818 0.2329 RANDOM 30.208
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] 1 -1.3 -1.44 0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.112 r_dihedral_angle_3_deg 15.242 r_dihedral_angle_4_deg 12.932 r_long_range_B_refined 6.035 r_long_range_B_other 5.989 r_dihedral_angle_1_deg 5.022 r_scangle_other 4.489 r_mcangle_other 2.96 r_mcangle_it 2.959 r_scbond_it 2.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.112 r_dihedral_angle_3_deg 15.242 r_dihedral_angle_4_deg 12.932 r_long_range_B_refined 6.035 r_long_range_B_other 5.989 r_dihedral_angle_1_deg 5.022 r_scangle_other 4.489 r_mcangle_other 2.96 r_mcangle_it 2.959 r_scbond_it 2.796 r_scbond_other 2.792 r_mcbond_it 1.97 r_mcbond_other 1.965 r_angle_refined_deg 1.906 r_angle_other_deg 1.123 r_chiral_restr 0.086 r_bond_refined_d 0.012 r_gen_planes_other 0.01 r_gen_planes_refined 0.009 r_bond_other_d 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3493 Nucleic Acid Atoms Solvent Atoms 173 Heterogen Atoms 91
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing