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W. succinogenes NrfA Y218F
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FS7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.7 293 PEG 4000, ammonium sulfate, yttrium chloride, acetate buffer, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.03 59.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.03 α = 90 b = 120.03 β = 90 c = 186.276 γ = 90
Symmetry Space Group I 41 2 2
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 MARMOSAIC 225 mm CCD 2007-09-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X12 0.9785 EMBL/DESY, HAMBURG X12
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 1.5 50 99.4 0.122 14.4 7.2 109091 108437 2 2
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) 1.5 1.6 97.1 0.663 2.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Cut-off Sigma (F) 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 1FS7 1.5 42.45 2 2 109091 102080 5396 98.71 0.18259 0.18088 0.1727 0.21506 0.2002 RANDOM 24.62
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] 0.15 0.15 -0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.5 r_dihedral_angle_4_deg 18.687 r_dihedral_angle_3_deg 14.057 r_dihedral_angle_1_deg 6.356 r_sphericity_free 5.426 r_scangle_it 4.031 r_sphericity_bonded 3.808 r_scbond_it 3.54 r_rigid_bond_restr 3.418 r_mcangle_it 1.903
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.5 r_dihedral_angle_4_deg 18.687 r_dihedral_angle_3_deg 14.057 r_dihedral_angle_1_deg 6.356 r_sphericity_free 5.426 r_scangle_it 4.031 r_sphericity_bonded 3.808 r_scbond_it 3.54 r_rigid_bond_restr 3.418 r_mcangle_it 1.903 r_angle_refined_deg 1.48 r_mcbond_it 1.302 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.306 r_nbd_refined 0.261 r_symmetry_vdw_refined 0.231 r_symmetry_metal_ion_refined 0.204 r_metal_ion_refined 0.155 r_xyhbond_nbd_refined 0.153 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_other r_mcbond_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3807 Nucleic Acid Atoms Solvent Atoms 649 Heterogen Atoms 242
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing