☰ Navigation Tabs
NO-bound copper nitrite reductase from Bradyrhizobium sp. ORS 375 (two-domain) at 1.19 A resolution (unrestrained, full matrix refinement by SHELX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6THF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 291 1.6/1.8 M (NH4)2SO3 and 50mM HEPES buffer pH 5/ pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.6 56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 107.467 α = 90 b = 107.467 β = 90 c = 107.467 γ = 90
Symmetry Space Group P 21 3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS EIGER X 9M 2020-02-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 0.8000 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.19 48.06 99.9 0.055 0.066 0.025 1 16.7 6.8 166484
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.19 1.21 97.9 1.223 1.476 0.572 0.508 1.4 6.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) 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 FREE R-VALUE 6THF 1.19 30 125178 125178 6588 99.9 0.125 0.125 0.1347 0.155 0.1396 RANDOM 19.327
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]
RMS Deviations Key Refinement Restraint Deviation s_bond_d s_angle_d s_similar_dist s_from_restr_planes s_zero_chiral_vol s_non_zero_chiral_vol s_anti_bump_dis_restr s_rigid_bond_adp_cmpnt s_similar_adp_cmpnt s_approx_iso_adps
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2663 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 157
Software Software Software Name Purpose SHELX refinement XDS data reduction XDS data scaling MOLREP phasing