☰ Navigation Tabs
Crystal structure of non-heme iron oxygenase OrfP in complex with Fe, succinate, and (3R,4R)-dihydroxy-L-Arg
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WBO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 100mM Bis Tris Propane, 200mM NaF, 20% PEG 3350, pH 7.5, VAPOR DIFFUSION, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.28 46.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.287 α = 90 b = 116.211 β = 91.66 c = 96.163 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 80 CCD ADSC QUANTUM 210r 2013-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL12B2 1 SPring-8 BL12B2
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 2.39 30 99.8 58611 55626 2 2
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 2.39 2.48 100
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 2WBO 2.39 26.15 58611 55626 2963 99.69 0.21656 0.21364 0.2179 0.27074 0.2804 RANDOM 56.348
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] 6.83 -0.88 -2.06 -4.73
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.485 r_dihedral_angle_4_deg 15.941 r_dihedral_angle_3_deg 15.891 r_dihedral_angle_1_deg 5.378 r_angle_refined_deg 1.06 r_angle_other_deg 0.776 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_bond_other_d 0.005 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.485 r_dihedral_angle_4_deg 15.941 r_dihedral_angle_3_deg 15.891 r_dihedral_angle_1_deg 5.378 r_angle_refined_deg 1.06 r_angle_other_deg 0.776 r_chiral_restr 0.058 r_bond_refined_d 0.006 r_bond_other_d 0.005 r_gen_planes_refined 0.004 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10518 Nucleic Acid Atoms Solvent Atoms 440 Heterogen Atoms 64
Software Software Software Name Purpose HKL-2000 data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling