☰ Navigation Tabs
C. jejuni NrfA Nitrite Complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other low res model, SAD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 38% PEG 1000, 100 mM CHES/NAOH, pH9, Strontium chloride, Nitrite soak in 38% PEG 1000, 100 mM Tris/HCl, pH 7.0, 100 mM Sodium Nitrite
Crystal Properties Matthews coefficient Solvent content 2.12 41.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.462 α = 90 b = 160.753 β = 118.12 c = 65.308 γ = 90
Symmetry Space Group P 1 21 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+ VariMax 2013-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2.29 80.38 93.7 0.158 0.192 3.8 2.95 49340
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.29 2.37 86.4 0.442 0.533 2.95
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 2.29 80.38 46789 2514 93.67 0.22315 0.22155 0.2282 0.25218 0.2568 RANDOM 38.638
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] -1.41 -0.23 0.97 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.947 r_dihedral_angle_4_deg 15.351 r_dihedral_angle_3_deg 15.326 r_dihedral_angle_1_deg 5.652 r_long_range_B_refined 4.587 r_long_range_B_other 4.587 r_mcangle_it 2.217 r_mcangle_other 2.217 r_scangle_other 2.054 r_mcbond_it 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.947 r_dihedral_angle_4_deg 15.351 r_dihedral_angle_3_deg 15.326 r_dihedral_angle_1_deg 5.652 r_long_range_B_refined 4.587 r_long_range_B_other 4.587 r_mcangle_it 2.217 r_mcangle_other 2.217 r_scangle_other 2.054 r_mcbond_it 1.34 r_mcbond_other 1.34 r_angle_refined_deg 1.31 r_scbond_it 1.226 r_scbond_other 1.226 r_angle_other_deg 0.769 r_chiral_restr 0.092 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 r_gen_planes_other 0.007 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9434 Nucleic Acid Atoms Solvent Atoms 257 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement d*TREK data scaling d*TREK data reduction MOLREP phasing PDB_EXTRACT data extraction