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Tudor domain of TDRD3 in complex with a small molecule
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3PMT pdb entry 3pmt
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291 1.2 M sodium citrate, 0.1 M Tris-HCl, pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.14 42.53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.855 α = 90 b = 83.855 β = 90 c = 114.045 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 CCD RAYONIX MX-300 2015-05-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 2.15 44.85 99.8 0.104 0.109 0.998 18.9 11.1 8558
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.15 2.22 98 0.982 1.03 0.884 11.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 pdb entry 3pmt 2.154 44.849 8557 699 99.837 0.198 0.1955 0.2011 0.2289 0.2362 42.789
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] 0.99 0.495 0.99 -3.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.964 r_dihedral_angle_3_deg 15.978 r_dihedral_angle_1_deg 8.607 r_lrange_other 7.143 r_lrange_it 7.142 r_scangle_it 5.385 r_scangle_other 5.381 r_mcangle_it 4.398 r_mcangle_other 4.394 r_scbond_it 3.888
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.964 r_dihedral_angle_3_deg 15.978 r_dihedral_angle_1_deg 8.607 r_lrange_other 7.143 r_lrange_it 7.142 r_scangle_it 5.385 r_scangle_other 5.381 r_mcangle_it 4.398 r_mcangle_other 4.394 r_scbond_it 3.888 r_scbond_other 3.885 r_mcbond_it 3.382 r_mcbond_other 3.379 r_angle_refined_deg 2.025 r_angle_other_deg 1.411 r_symmetry_xyhbond_nbd_refined 0.333 r_symmetry_nbd_refined 0.199 r_nbd_refined 0.187 r_nbtor_refined 0.186 r_nbd_other 0.184 r_symmetry_nbd_other 0.183 r_xyhbond_nbd_refined 0.133 r_chiral_restr 0.099 r_symmetry_nbtor_other 0.092 r_bond_refined_d 0.017 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 868 Nucleic Acid Atoms Solvent Atoms 11 Heterogen Atoms 45
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction PHASER phasing SCALEPACK data scaling Aimless data scaling