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Serial Cu nitrite reductase structures at elevated cryogenic temperature, 240K. Dataset 1.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BW4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 0.1 M sodium citrate at pH 5.0 and 1.6 M ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.02 39.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.13 α = 90 b = 96.13 β = 90 c = 96.13 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 240 PIXEL DECTRIS PILATUS 6M 2016-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.97690 CHESS F1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.38 28.98 97.1 0.109 0.067 0.99 7 4.1 59054
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.38 1.4 69.2 0.529 1.1 1.7
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 MOLECULAR REPLACEMENT THROUGHOUT 2BW4 1.38 28.98 56094 2926 96.89 0.11851 0.11656 0.1168 0.15582 0.1556 RANDOM 12.719
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 r_dihedral_angle_2_deg 34.99 r_sphericity_free 27.513 r_dihedral_angle_4_deg 18.766 r_dihedral_angle_3_deg 11.866 r_sphericity_bonded 8.386 r_dihedral_angle_1_deg 8.025 r_long_range_B_refined 3.961 r_long_range_B_other 3.686 r_scangle_other 2.872 r_scbond_it 2.572
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.99 r_sphericity_free 27.513 r_dihedral_angle_4_deg 18.766 r_dihedral_angle_3_deg 11.866 r_sphericity_bonded 8.386 r_dihedral_angle_1_deg 8.025 r_long_range_B_refined 3.961 r_long_range_B_other 3.686 r_scangle_other 2.872 r_scbond_it 2.572 r_mcangle_other 2.505 r_mcangle_it 2.5 r_scbond_other 2.414 r_rigid_bond_restr 2.121 r_mcbond_it 2.021 r_angle_refined_deg 1.741 r_mcbond_other 1.69 r_angle_other_deg 1.03 r_chiral_restr 0.12 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_gen_planes_other 0.004 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2574 Nucleic Acid Atoms Solvent Atoms 300 Heterogen Atoms 32
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing