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XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with N00572d (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 -- 12% PEG8K
Crystal Properties Matthews coefficient Solvent content 2.1 41.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.94 α = 90 b = 27.52 β = 100.19 c = 56.73 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 1.18 55.84 95 0.033 0.041 0.023 0.999 16.5 2.8 39796
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 1.18 1.21 77.9 0.602 0.805 0.53 0.691 1.6 2375
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 1.18 55.84 37830 1964 94.91 0.1642 0.163 0.1669 0.1867 0.1914 RANDOM 16.158
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] 0.91 0.81 -0.46 -0.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.386 r_dihedral_angle_4_deg 19.021 r_dihedral_angle_3_deg 11.922 r_dihedral_angle_1_deg 5.092 r_rigid_bond_restr 2.667 r_angle_refined_deg 1.822 r_mcangle_it 1.785 r_angle_other_deg 1.503 r_mcbond_it 1.476 r_mcbond_other 1.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.386 r_dihedral_angle_4_deg 19.021 r_dihedral_angle_3_deg 11.922 r_dihedral_angle_1_deg 5.092 r_rigid_bond_restr 2.667 r_angle_refined_deg 1.822 r_mcangle_it 1.785 r_angle_other_deg 1.503 r_mcbond_it 1.476 r_mcbond_other 1.375 r_chiral_restr 0.092 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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 126 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing