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Tudor Domain of Tumor suppressor p53BP1 with small molecule ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G3R PDB ENTRY 2G3R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 293 19% PEG3350, 0.15 M DL-malic acid, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.73 54.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.548 α = 90 b = 100.458 β = 90 c = 83.348 γ = 90
Symmetry Space Group C 2 2 21
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 315r 2014-06-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.97918 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 1.5 50 98.1 0.049 9.9 7.8 48740
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 1.5 1.53 82.9 0.67 5.8 2040
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 ENTRY 2G3R 1.5 50 47270 1433 98.02 0.1977 0.1971 0.2201 0.224 RANDOM 28.845
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] -1.25 2.93 -1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.94 r_dihedral_angle_4_deg 17.393 r_dihedral_angle_3_deg 12.667 r_dihedral_angle_1_deg 6.589 r_mcangle_it 2.674 r_mcbond_it 1.723 r_mcbond_other 1.722 r_angle_refined_deg 1.339 r_angle_other_deg 0.735 r_chiral_restr 0.083
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.94 r_dihedral_angle_4_deg 17.393 r_dihedral_angle_3_deg 12.667 r_dihedral_angle_1_deg 6.589 r_mcangle_it 2.674 r_mcbond_it 1.723 r_mcbond_other 1.722 r_angle_refined_deg 1.339 r_angle_other_deg 0.735 r_chiral_restr 0.083 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1886 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 42
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 Coot model building GRADE refinement