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E. coli NfsA with hydroquinone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F5V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 28% PEG 3,000; 100 mM imidazole pH 7.0;
20% DMSO,25 mM hydroxyquinone
Crystal Properties Matthews coefficient Solvent content 2.07 40.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 91.985 α = 90 b = 52.022 β = 134.16 c = 64.77 γ = 90
Symmetry Space Group C 1 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 100 CCD RIGAKU SATURN 944 2011-05-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.54
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 1.25 46.46 97.6 0.05 19.2 6.39 59285
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) 1 1.25 1.35 84.9 0.54 2.4
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 1F5V 1.25 46.03 56273 2974 97.63 0.1248 0.1232 0.1215 0.1549 0.1539 RANDOM 16.149
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] -0.32 0.17 -1.08 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.773 r_dihedral_angle_4_deg 20.026 r_dihedral_angle_3_deg 11.315 r_dihedral_angle_1_deg 5.829 r_rigid_bond_restr 1.799 r_angle_refined_deg 1.496 r_angle_other_deg 1.197 r_chiral_restr 0.101 r_bond_refined_d 0.01 r_gen_planes_refined 0.009
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.773 r_dihedral_angle_4_deg 20.026 r_dihedral_angle_3_deg 11.315 r_dihedral_angle_1_deg 5.829 r_rigid_bond_restr 1.799 r_angle_refined_deg 1.496 r_angle_other_deg 1.197 r_chiral_restr 0.101 r_bond_refined_d 0.01 r_gen_planes_refined 0.009 r_gen_planes_other 0.002 r_bond_other_d 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1875 Nucleic Acid Atoms Solvent Atoms 298 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction MOSFLM data reduction SCALA data scaling PHASER phasing