☰ Navigation Tabs
Crystal structure of KSHV KicGAS/ORF52
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2OA5
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 289 1 microL of protein (10 mg/ml) + 1 microL of reservoir solution of 9% (v/v) PEG3350, 100mM Na-citrate pH 4.5 + 0.2microL of the detergent additive n-Octyl-N,N-dimethyl-3-ammonio-1-propanesulfonate
Crystal Properties Matthews coefficient Solvent content 2.81 56.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.332 α = 90 b = 58.683 β = 90 c = 138.421 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 80 PIXEL DECTRIS EIGER X 9M 2020-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-1 0.9795 NSLS-II 17-ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Rrim I (All) 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 2.4 50 98.3 0.128 0.102 0.142 0.062 0.991 19.78 4.9 15886 52.29
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.49 90.4 0.595 0.497 0.696 0.351 0.751 1.32 2.9
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 2OA5 2.5 49.77 1.38 14384 1442 98.95 0.2286 0.2246 0.2361 0.265 0.2771 64.27
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 17.6757 f_angle_d 0.5047 f_chiral_restr 0.032 f_plane_restr 0.0029 f_bond_d 0.0023
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1282 Nucleic Acid Atoms Solvent Atoms 46 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing