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Crystal structure of the rat heme oxygenase (HO-1) in complex with heme binding dithioerythritol (DTE)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3I9T PDB ENTRY 3I9T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.4 293 3.2M sodium formate, 10mM sodium azide, 5mM DTV, pH7.4, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.882 α = 90 b = 65.882 β = 90 c = 120.244 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 95 CCD ADSC QUANTUM 4r 2006-02-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-6A 1 Photon Factory BL-6A
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 2.25 50 99.9 0.062 32.1 7.2 14964 30.585
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) 2.25 2.33 99.9 0.329 7.04 7.3 1454
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 3I9T 2.25 30 14140 754 99.98 0.16961 0.16683 0.1756 0.22266 0.2353 RANDOM 29.132
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] 1.76 0.88 1.76 -2.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.719 r_dihedral_angle_3_deg 16.255 r_dihedral_angle_4_deg 15.26 r_dihedral_angle_1_deg 5.673 r_scangle_it 5.026 r_scbond_it 3.17 r_angle_refined_deg 1.913 r_mcangle_it 1.912 r_mcbond_it 1.06 r_chiral_restr 0.129
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.719 r_dihedral_angle_3_deg 16.255 r_dihedral_angle_4_deg 15.26 r_dihedral_angle_1_deg 5.673 r_scangle_it 5.026 r_scbond_it 3.17 r_angle_refined_deg 1.913 r_mcangle_it 1.912 r_mcbond_it 1.06 r_chiral_restr 0.129 r_bond_refined_d 0.024 r_gen_planes_refined 0.01 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 1711 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms 51
Software Software Software Name Purpose CNS refinement REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling CNS phasing