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W. succinogenes NrfA Y218F Sulfite Complex
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 aulfate, yttrium chloride, acetate buffer, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.98 58.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 119.4 α = 90 b = 119.4 β = 90 c = 184.789 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 1.3 50 98.3 0.114 15.3 6.9 164396 161601 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) 1.3 1.39 93.5 0.25 2
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 1.3 40.39 2 2 164396 153357 8132 98.43 0.18262 0.18128 0.2699 0.20778 0.2853 RANDOM 23.748
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] 0.47 0.47 -0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.321 r_dihedral_angle_4_deg 21.294 r_dihedral_angle_3_deg 12.962 r_dihedral_angle_1_deg 5.882 r_sphericity_free 4.066 r_sphericity_bonded 3.915 r_scangle_it 3.227 r_scbond_it 2.33 r_mcangle_it 1.535 r_rigid_bond_restr 1.438
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.321 r_dihedral_angle_4_deg 21.294 r_dihedral_angle_3_deg 12.962 r_dihedral_angle_1_deg 5.882 r_sphericity_free 4.066 r_sphericity_bonded 3.915 r_scangle_it 3.227 r_scbond_it 2.33 r_mcangle_it 1.535 r_rigid_bond_restr 1.438 r_angle_refined_deg 1.326 r_mcbond_it 1 r_nbtor_refined 0.313 r_nbd_refined 0.254 r_symmetry_vdw_refined 0.199 r_metal_ion_refined 0.173 r_symmetry_hbond_refined 0.141 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.086 r_symmetry_metal_ion_refined 0.069 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 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 3802 Nucleic Acid Atoms Solvent Atoms 714 Heterogen Atoms 240
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing