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Crystal structure of heme oxygenase-2 from Synechocystis sp. PCC 6803 in complex with heme
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1DVE PDB ENTRY 1DVE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 pottasium sodium tartrate, pottasium phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.6 52.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.163 α = 90 b = 74.585 β = 108.15 c = 72.661 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 MARRESEARCH 2004-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.063 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.75 20 89.2 53138 53138
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.84 93
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 (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1DVE 1.75 19.76 50464 50464 2674 89.25 0.19818 0.19818 0.19318 0.25374 0.2522 RANDOM 19.087
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] -0.02 -0.02 -0.01 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.515 r_scangle_it 6.647 r_scbond_it 4.746 r_mcangle_it 3.023 r_mcbond_it 2.142 r_angle_refined_deg 1.871 r_angle_other_deg 1.209 r_symmetry_hbond_refined 0.338 r_symmetry_vdw_other 0.301 r_xyhbond_nbd_refined 0.287
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 7.515 r_scangle_it 6.647 r_scbond_it 4.746 r_mcangle_it 3.023 r_mcbond_it 2.142 r_angle_refined_deg 1.871 r_angle_other_deg 1.209 r_symmetry_hbond_refined 0.338 r_symmetry_vdw_other 0.301 r_xyhbond_nbd_refined 0.287 r_nbd_refined 0.284 r_nbd_other 0.263 r_symmetry_vdw_refined 0.213 r_chiral_restr 0.118 r_nbtor_other 0.092 r_gen_planes_other 0.047 r_metal_ion_refined 0.041 r_gen_planes_refined 0.034 r_bond_refined_d 0.024 r_bond_other_d 0.021 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_other r_symmetry_hbond_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 3917 Nucleic Acid Atoms Solvent Atoms 634 Heterogen Atoms 86
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling MOLREP phasing