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2-Oxoacid:Ferredoxin Oxidoreductase 1 from Sulfolobus tokodai
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5B46
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 298 15% PEG3350, 0.1 M Tris-HCl, 0.1 M NaBr
Crystal Properties Matthews coefficient Solvent content 2.25 45.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 75.15 α = 90 b = 145.878 β = 90 c = 170.094 γ = 90
Symmetry Space Group P 21 21 21
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 4r 2005-12-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.9780 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 2.5 50 99.2 0.058 27 4.3 65171
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 2.5 2.59 93.7 0.373 1.72 3.1
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 5B46 2.5 36.47 61283 3274 98.92 0.21466 0.21121 0.2122 0.27799 0.2737 RANDOM 67.549
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.258 r_dihedral_angle_3_deg 19.755 r_dihedral_angle_4_deg 17.32 r_long_range_B_refined 10.914 r_long_range_B_other 10.914 r_scangle_other 8.061 r_dihedral_angle_1_deg 7.337 r_mcangle_it 7.047 r_mcangle_other 7.046 r_scbond_it 5.236
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.258 r_dihedral_angle_3_deg 19.755 r_dihedral_angle_4_deg 17.32 r_long_range_B_refined 10.914 r_long_range_B_other 10.914 r_scangle_other 8.061 r_dihedral_angle_1_deg 7.337 r_mcangle_it 7.047 r_mcangle_other 7.046 r_scbond_it 5.236 r_scbond_other 5.236 r_mcbond_it 4.75 r_mcbond_other 4.75 r_angle_refined_deg 1.762 r_angle_other_deg 1.106 r_chiral_restr 0.101 r_bond_refined_d 0.013 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 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 12972 Nucleic Acid Atoms Solvent Atoms 61 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing