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Crystal Structure of the tudor domain of human TDRD3 in complex with an anti-TDRD3 FAB
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2HFF pdb entries 2HFF (modified on FFAS03 server) and 3PMT experimental model PDB 3PMT pdb entries 2HFF (modified on FFAS03 server) and 3PMT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 16% PEG-3350, 0.05M citric acid, 0.05M bis-tris propane, vapor diffusion, sitting drop, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.35 47.55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.708 α = 80.96 b = 93.726 β = 82.82 c = 159.932 γ = 90.06
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 ADSC QUANTUM 315 2010-08-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97924 APS 19-ID
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 2.05 50 97.4 0.086 6.4 2.5 266201
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 2.05 2.12 93.1 0.414 2.3 25457
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entries 2HFF (modified on FFAS03 server) and 3PMT 2.05 30 266095 2162 97.202 0.224 0.2233 0.2635 0.2918 thin shells (SFTOOLS) 45.03
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] -1.951 -0.248 0.076 0.537 -2.489 2.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.294 r_dihedral_angle_4_deg 19.749 r_dihedral_angle_3_deg 13.334 r_dihedral_angle_1_deg 7.101 r_scangle_it 3.16 r_scbond_it 2.03 r_mcangle_it 1.338 r_angle_refined_deg 1.267 r_angle_other_deg 0.879 r_mcbond_it 0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.294 r_dihedral_angle_4_deg 19.749 r_dihedral_angle_3_deg 13.334 r_dihedral_angle_1_deg 7.101 r_scangle_it 3.16 r_scbond_it 2.03 r_mcangle_it 1.338 r_angle_refined_deg 1.267 r_angle_other_deg 0.879 r_mcbond_it 0.76 r_mcbond_other 0.175 r_chiral_restr 0.078 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 29516 Nucleic Acid Atoms Solvent Atoms 1275 Heterogen Atoms 143
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction SBC-Collect data collection HKL-3000 data reduction HKL-3000 data scaling