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XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with N00964e (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 2.09 41.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.58 α = 90 b = 27.47 β = 100.34 c = 56.76 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 1.29 55.84 98.5 0.057 0.069 0.038 0.998 14.2 3 31423
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 1.29 1.32 96.6 0.691 0.893 0.56 0.495 2.2 2238
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 1.29 55.84 29930 1493 98.29 0.1656 0.1639 0.1694 0.1998 0.2093 RANDOM 18.827
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] -0.82 1.59 -1.74 1.85
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.604 r_dihedral_angle_4_deg 12.837 r_rigid_bond_restr 12.69 r_dihedral_angle_3_deg 12.417 r_dihedral_angle_1_deg 5.545 r_mcangle_it 2.347 r_angle_refined_deg 2.062 r_mcbond_it 2.002 r_mcbond_other 1.981 r_angle_other_deg 1.602
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.604 r_dihedral_angle_4_deg 12.837 r_rigid_bond_restr 12.69 r_dihedral_angle_3_deg 12.417 r_dihedral_angle_1_deg 5.545 r_mcangle_it 2.347 r_angle_refined_deg 2.062 r_mcbond_it 2.002 r_mcbond_other 1.981 r_angle_other_deg 1.602 r_chiral_restr 0.126 r_bond_refined_d 0.016 r_gen_planes_refined 0.012 r_bond_other_d 0.006 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 990 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 8
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing