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Crystal structure of Trim25 Pspry
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6FLM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 277 100 mM Na citrate pH5.0 and 4 M NaCl
Crystal Properties Matthews coefficient Solvent content 3.92 68.62
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 182.015 α = 90 b = 182.015 β = 90 c = 221.32 γ = 120
Symmetry Space Group P 31 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 2018-10-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.698 50 100 0.138 3.9 6.7 116665
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.75 0.138
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.698 47.51 116574 5780 99.92 0.214 0.2117 0.2145 0.2648 0.2616 38.322
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] -0.717 -0.359 -0.717 2.326
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.601 r_dihedral_angle_4_deg 24.972 r_dihedral_angle_3_deg 20.981 r_dihedral_angle_1_deg 8.603 r_lrange_other 8.305 r_lrange_it 8.304 r_mcangle_it 5.606 r_mcangle_other 5.606 r_scangle_it 5.571 r_scangle_other 5.571
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.601 r_dihedral_angle_4_deg 24.972 r_dihedral_angle_3_deg 20.981 r_dihedral_angle_1_deg 8.603 r_lrange_other 8.305 r_lrange_it 8.304 r_mcangle_it 5.606 r_mcangle_other 5.606 r_scangle_it 5.571 r_scangle_other 5.571 r_mcbond_it 3.469 r_mcbond_other 3.461 r_scbond_it 3.382 r_scbond_other 3.382 r_angle_refined_deg 1.635 r_angle_other_deg 1.203 r_nbd_refined 0.204 r_symmetry_nbd_other 0.195 r_xyhbond_nbd_refined 0.178 r_nbtor_refined 0.176 r_nbd_other 0.176 r_symmetry_nbd_refined 0.171 r_symmetry_xyhbond_nbd_refined 0.167 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_other 0.079 r_chiral_restr 0.067 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 18972 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing