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Tudor Domain of Tumor suppressor p53BP1 with MFP-2706
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4RG2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 2M ammonium sulfate, 0.1 M HEPES pH 7.5, 2% PEG 400
Crystal Properties Matthews coefficient Solvent content 2.9 57.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 125.05 α = 90 b = 125.05 β = 90 c = 125.05 γ = 90
Symmetry Space Group I 21 3
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 16M 2017-11-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 24-ID-E 0.97918 APS 24-ID-E
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.96 40 100 0.056 0.058 0.018 8.8 10.8 23455
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 1.96 1.99 100 0.95 1.002 0.314 0.729 10.1
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 4RG2 1.96 39.58 22255 1189 99.97 0.2238 0.2223 0.2329 0.2556 0.2591 RANDOM 40.417
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 r_dihedral_angle_2_deg 26.528 r_dihedral_angle_4_deg 16.507 r_dihedral_angle_3_deg 15.025 r_dihedral_angle_1_deg 8.027 r_angle_refined_deg 1.461 r_angle_other_deg 1.326 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 26.528 r_dihedral_angle_4_deg 16.507 r_dihedral_angle_3_deg 15.025 r_dihedral_angle_1_deg 8.027 r_angle_refined_deg 1.461 r_angle_other_deg 1.326 r_chiral_restr 0.065 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 1808 Nucleic Acid Atoms Solvent Atoms 90 Heterogen Atoms 19
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-3000 data reduction REFMAC phasing