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Structure of glutathione amide reductase from Chromatium gracile in complex with NAD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2R9Z Native GAR structure, PDB 2R9Z
Crystallization Crystal Properties Matthews coefficient Solvent content 2.96 58.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.989 α = 90 b = 71.989 β = 90 c = 224.603 γ = 90
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 120 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.8015 EMBL/DESY, HAMBURG X13
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 2.5 15 96.3 0.06 16.57 2.81 39389 39321
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 2.5 2.59 98.1 0.398 2.1 2.79 3835
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 used phases from 2R9Z directly THROUGHOUT Native GAR structure, PDB 2R9Z 2.5 15 35782 1888 95.81 0.18713 0.18466 0.1841 0.23324 0.2328 RANDOM 35.541
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] 0.63 0.63 -1.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.287 r_dihedral_angle_4_deg 20.632 r_dihedral_angle_3_deg 16.934 r_dihedral_angle_1_deg 5.706 r_scangle_it 1.762 r_angle_refined_deg 1.243 r_scbond_it 1.066 r_mcangle_it 0.687 r_mcbond_it 0.394 r_nbtor_refined 0.306
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.287 r_dihedral_angle_4_deg 20.632 r_dihedral_angle_3_deg 16.934 r_dihedral_angle_1_deg 5.706 r_scangle_it 1.762 r_angle_refined_deg 1.243 r_scbond_it 1.066 r_mcangle_it 0.687 r_mcbond_it 0.394 r_nbtor_refined 0.306 r_symmetry_hbond_refined 0.238 r_symmetry_vdw_refined 0.229 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.142 r_chiral_restr 0.079 r_metal_ion_refined 0.046 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 6685 Nucleic Acid Atoms Solvent Atoms 474 Heterogen Atoms 206
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling CCP4 phasing