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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 PDB 6EMS SPOUT domain of PDB ID 6EMS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5 298 20 % PEG 3350, 8% v/v Tascimate
Crystal Properties Matthews coefficient Solvent content 2.55 51.73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.262 α = 90 b = 62.262 β = 90 c = 203.51 γ = 120
Symmetry Space Group P 61 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 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 1.794 47.645 99.8 0.09092 0.092179 0.0149 1 30.85 37.9 22813 34.5407666018
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 1.8 1.9 97.87 2.361 2.394 0.3871 0.763 1.63 36.5
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 SPOUT domain of PDB ID 6EMS 1.794 47.645 1.3634 22807 1140 99.7637898605 0.1921 0.1914 0.1963 0.2062 0.2096 RANDOM 45.0339235129
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 13.5365816251 f_angle_d 0.515417634352 f_chiral_restr 0.0444691270129 f_bond_d 0.00300662997119 f_plane_restr 0.00236177992714
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1347 Nucleic Acid Atoms Solvent Atoms 113 Heterogen Atoms 52
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing