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XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with N00804d (space group C2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7AV9 7AV9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 277 0.04M potassium phosphate monobasic -- 8% PEG8K
Crystal Properties Matthews coefficient Solvent content 2.07 40.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.01 α = 90 b = 27.15 β = 100.46 c = 56.63 γ = 90
Symmetry Space Group C 1 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 2016-06-23 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 1.19 40.82 92.7 0.037 0.045 0.025 0.999 14.2 2.8 37327
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 1.19 1.22 74.3 0.529 0.718 0.482 0.768 1.9 2157
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 7AV9 1.19 40.82 35449 1858 92.62 0.1697 0.1682 0.17 0.1984 0.2007 RANDOM 18.076
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] -0.31 0.94 0.66 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.149 r_dihedral_angle_4_deg 15.343 r_dihedral_angle_3_deg 13.94 r_dihedral_angle_1_deg 5.135 r_rigid_bond_restr 3.161 r_mcangle_it 2.074 r_angle_refined_deg 1.825 r_mcbond_it 1.808 r_mcbond_other 1.727 r_angle_other_deg 1.569
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.149 r_dihedral_angle_4_deg 15.343 r_dihedral_angle_3_deg 13.94 r_dihedral_angle_1_deg 5.135 r_rigid_bond_restr 3.161 r_mcangle_it 2.074 r_angle_refined_deg 1.825 r_mcbond_it 1.808 r_mcbond_other 1.727 r_angle_other_deg 1.569 r_chiral_restr 0.108 r_bond_refined_d 0.013 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 990 Nucleic Acid Atoms Solvent Atoms 160 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing