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Structure of VIM-2 with 2-Mercaptomethyl-thiazolidine L-anti-1b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BZ3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.2 M MAGNESIUM FORMATE, 20 % W/V PEG3350
Crystal Properties Matthews coefficient Solvent content 2.03 39.38
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.48 α = 90 b = 79.17 β = 90.495 c = 78.07 γ = 90
Symmetry Space Group I 1 2 1
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 PILATUS 6M-F 2017-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91588 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.4 55.59 99.7 0.077 0.986 4.8 5.1 80433
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.4 1.42 0.357 0.567 2
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 4BZ3 1.40001375561 55.587604555 71.9010155309 80183 3908 99.4073963873 0.154298105135 0.149734464045 0.1491 0.176227683252 0.1709 20.1785883793
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 15.4213056306 f_angle_d 1.24835306045 f_chiral_restr 0.10275642905 f_bond_d 0.0133151768595 f_plane_restr 0.0077213187091
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3486 Nucleic Acid Atoms Solvent Atoms 491 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement MOSFLM data reduction Aimless data scaling PHASER phasing