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Structure of oxidized VIM-20
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4NQ2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.6 298 0.17 M ammonium acetate, 0.085 M Sodium Acetate, 25.5 % (w/v) PEG 4000, and 15 % (v/v) glycerol
Crystal Properties Matthews coefficient Solvent content 2.12 38.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.86 α = 90 b = 77.86 β = 90 c = 79.36 γ = 90
Symmetry Space Group I 2 2 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CMOS RDI CMOS_8M 2019-03-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0000 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.37 39.68 99.9 0.99 19.2 9.1 84110 15.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.37 1.42 99.9 0.71 1.4 6.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 4NQ2 1.37 39.68 1.35 84110 3245 99.91 0.1637 0.1625 0.1631 0.1918 0.1914 Random selection
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 f_dihedral_angle_d 19.054 f_angle_d 0.807 f_chiral_restr 0.079 f_bond_d 0.005 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1693 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 14
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing