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E. coli NfsA with Fumarate
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 7 291 100 mM imidazole pH 7,
26 % PEG 3,000
30 mM Fumarate
Crystal Properties Matthews coefficient Solvent content 2.09 41.08
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.061 α = 90 b = 52.237 β = 134.17 c = 64.957 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 70 2009-09-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 1.247 46.6 93.5 0.043 26.1 8.69 57570
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 1.247 1.28 61.16 0.4 3.7
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 46.59 54665 2903 93.55 0.1075 0.1062 0.1055 0.1325 0.1324 RANDOM 15.324
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] 0.31 0.33 -1.18 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.209 r_dihedral_angle_4_deg 19.401 r_dihedral_angle_3_deg 12.271 r_dihedral_angle_1_deg 5.68 r_rigid_bond_restr 1.428 r_angle_refined_deg 1.283 r_angle_other_deg 1.173 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.007
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.209 r_dihedral_angle_4_deg 19.401 r_dihedral_angle_3_deg 12.271 r_dihedral_angle_1_deg 5.68 r_rigid_bond_restr 1.428 r_angle_refined_deg 1.283 r_angle_other_deg 1.173 r_chiral_restr 0.079 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 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 1887 Nucleic Acid Atoms Solvent Atoms 328 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing