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Copper nitrite reductase from Achromobacter cycloclastes: small cell polymorph 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 2.5 M ammonium sulphate, 0.1 M sodium citrate pH 4.5 buffer, in a ratio of 1:3 and mixed by vortexing for 60 seconds. Microcrystals with a diameter of 5-15 microns grew at room temperature over a period of 4-6 days.
Crystal Properties Matthews coefficient Solvent content 2.04 39.79
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.382 α = 90 b = 96.382 β = 90 c = 96.382 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 29.06 100 0.996 0.0571 1.75 548 49882 16.6
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 0.726 0.8773 0.17 206.5
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 29.06 47321 2561 99.98 0.1873 0.1858 0.1556 0.2164 0.1802 RANDOM 22.284
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 37.643 r_dihedral_angle_4_deg 16.488 r_dihedral_angle_3_deg 14.408 r_dihedral_angle_1_deg 7.488 r_angle_other_deg 3.828 r_mcangle_it 2.109 r_angle_refined_deg 1.641 r_mcbond_it 1.332 r_mcbond_other 1.331 r_chiral_restr 0.091
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.643 r_dihedral_angle_4_deg 16.488 r_dihedral_angle_3_deg 14.408 r_dihedral_angle_1_deg 7.488 r_angle_other_deg 3.828 r_mcangle_it 2.109 r_angle_refined_deg 1.641 r_mcbond_it 1.332 r_mcbond_other 1.331 r_chiral_restr 0.091 r_bond_refined_d 0.013 r_gen_planes_other 0.008 r_gen_planes_refined 0.007 r_bond_other_d
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2538 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 5
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction DIALS data scaling PHASER phasing