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Crystal Structure of dual specific Trm10 construct from Thermococcus kodakaraensis.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Crystal structure of TkTrm10 construct ( to be deposited)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 293 10% PEG6000, 0.2M LiCl and 0.1M NaAc pH 5.5
Crystal Properties Matthews coefficient Solvent content 2.08 40.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.084 α = 90 b = 71.084 β = 90 c = 191.958 γ = 120
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 EIGER X 9M 2016-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SOLEIL BEAMLINE PROXIMA 2 0.9801 SOLEIL PROXIMA 2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 2.29745444787 44.3625637794 99.81 0.1132 0.1161 0.02533 1 20.55 21 24345 55.0685253935
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.4 98.12 1.946 1.9996 0.4367 0.577 1.45 20.4
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 THROUGHOUT Crystal structure of TkTrm10 construct ( to be deposited) 2.29745444787 44.3625637794 1.38327623631 24332 1216 99.7581074987 0.196891010953 0.195472590493 0.2039 0.222729264961 0.2263 Random 68.9272527311
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 12.6241556608 f_angle_d 0.52478990995 f_chiral_restr 0.0457912640862 f_plane_restr 0.00257300626663 f_bond_d 0.00200054821472
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3986 Nucleic Acid Atoms Solvent Atoms 78 Heterogen Atoms 93
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing