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Structure of IMP-1 with 2-Mercaptomethyl-thiazolidine D-syn-1b
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5HH4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 292 0.1 M sodium cacodylate pH 6.0, 0.2 M sodium acetate, 25% PEG 8000. 1ul protein (25 mg/ml) mixed with 1 ul reagent.
Crystal Properties Matthews coefficient Solvent content 2.46 50.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.7824 α = 90 b = 77.9686 β = 90 c = 261.906 γ = 90
Symmetry Space Group P 21 21 21
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 2017-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.97949 Diamond I04
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 1.87 58.153 100 0.026 0.999 18.6 26.2 83944 28.727022947
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 1.87 1.91 0.469 0.784 1.8
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5HH4 1.8700095823 58.1529684507 1.32910924106 83742 4049 99.8795367532 0.175417928252 0.174089105023 0.18 0.201348319116 0.2065 41.0579551912
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 14.4692503847 f_angle_d 1.32061608309 f_chiral_restr 0.0883731345638 f_plane_restr 0.0145893801033 f_bond_d 0.011621317517
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6863 Nucleic Acid Atoms Solvent Atoms 492 Heterogen Atoms 88
Software Software Software Name Purpose PHENIX refinement DIALS data reduction Aimless data scaling PHASER phasing