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W. succinogenes NrfA Y218F Nitrite 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 sulfate, yttrium chloride, acetate buffer, pH 5.7, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.08 60.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 120.768 α = 90 b = 120.768 β = 90 c = 186.466 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 IMAGE PLATE MAR scanner 345 mm plate 2007-09-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 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 1.75 30 99.8 0.11 12.2 7.2 69720 69581 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) 1.75 1.85 99.2 0.687 2.1
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 (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 1.75 29.49 2 2 65830 3543 99.53 0.17908 0.17719 0.1754 0.2148 0.213 RANDOM 29.209
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] 0.58 0.58 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_dihedral_angle_4_deg 22.519 r_dihedral_angle_3_deg 13.764 r_dihedral_angle_1_deg 6.071 r_scangle_it 3.082 r_scbond_it 2.119 r_angle_refined_deg 1.398 r_mcangle_it 1.279 r_mcbond_it 0.822 r_nbtor_refined 0.293
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.899 r_dihedral_angle_4_deg 22.519 r_dihedral_angle_3_deg 13.764 r_dihedral_angle_1_deg 6.071 r_scangle_it 3.082 r_scbond_it 2.119 r_angle_refined_deg 1.398 r_mcangle_it 1.279 r_mcbond_it 0.822 r_nbtor_refined 0.293 r_nbd_refined 0.248 r_symmetry_vdw_refined 0.248 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.149 r_chiral_restr 0.103 r_metal_ion_refined 0.07 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3894 Nucleic Acid Atoms Solvent Atoms 646 Heterogen Atoms 235
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection DENZO data reduction SCALEPACK data scaling MOLREP phasing