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Copper nitrite reductase from Achromobacter cycloclastes: non-polymorph separated dataset 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5I6K
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 4.5 298 Batch microcrystals were prepared by rapidly mixing 20 mg/ml AcNiR in 20mM Tris, pH 7.5 with a solution containing 2.5M ammonium sulphate, 0.1M sodium citrate pH 4.5 - in a ratio of 1:3 and mixed by vortexing for 60s. Microcrystals with a diameter of 5-15 microns grew at room temperature over a periof of 4-6 days
Crystal Properties Matthews coefficient Solvent content 2.13 42.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.87 α = 90 b = 96.87 β = 90 c = 96.87 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 298 PIXEL DECTRIS PILATUS3 6M 2018-01-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.9686 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (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 1.48 29.21 100 0.997 0.0515 1.88 927 50616
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.51 100 0.552 0.545 0.15 302
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 5i6k 1.48 29.21 48121 2474 99.97 0.2371 0.23506 0.2307 0.27645 0.2703 RANDOM 24.407
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 36.956 r_dihedral_angle_4_deg 20.758 r_dihedral_angle_3_deg 16.451 r_dihedral_angle_1_deg 7.788 r_long_range_B_refined 4.399 r_long_range_B_other 4.392 r_scangle_other 2.784 r_mcangle_it 2.165 r_mcangle_other 2.164 r_scbond_it 1.764
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.956 r_dihedral_angle_4_deg 20.758 r_dihedral_angle_3_deg 16.451 r_dihedral_angle_1_deg 7.788 r_long_range_B_refined 4.399 r_long_range_B_other 4.392 r_scangle_other 2.784 r_mcangle_it 2.165 r_mcangle_other 2.164 r_scbond_it 1.764 r_scbond_other 1.759 r_angle_refined_deg 1.598 r_mcbond_it 1.366 r_mcbond_other 1.364 r_angle_other_deg 0.965 r_chiral_restr 0.09 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 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 2541 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling