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Crystal structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with compound-13 N11537 (SGC - Diamond I04-1 fragment screening)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MB3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1M HEPES pH 7.5 , 0.15M magnesium chloride , 32% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.12 41.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.17 α = 90 b = 91.4 β = 90 c = 23.99 γ = 90
Symmetry Space Group P 21 21 2
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 2M 2014-12-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.69 30.47 99.2 0.034 0.015 1 26.1 6.5 15419
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.73 99.4 0.85 0.347 0.866 2.5 6.8 1122
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 MOLECULAR REPLACEMENT THROUGHOUT 3MB3 1.69 30.47 14611 767 98.87 0.2195 0.2172 0.2245 0.2649 0.2719 RANDOM 33.491
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] -1.91 1.47 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.05 r_dihedral_angle_4_deg 16.857 r_dihedral_angle_3_deg 13.235 r_dihedral_angle_1_deg 4.473 r_mcangle_it 1.566 r_angle_refined_deg 1.324 r_angle_other_deg 0.978 r_mcbond_it 0.96 r_mcbond_other 0.959 r_chiral_restr 0.082
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.05 r_dihedral_angle_4_deg 16.857 r_dihedral_angle_3_deg 13.235 r_dihedral_angle_1_deg 4.473 r_mcangle_it 1.566 r_angle_refined_deg 1.324 r_angle_other_deg 0.978 r_mcbond_it 0.96 r_mcbond_other 0.959 r_chiral_restr 0.082 r_bond_refined_d 0.01 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 995 Nucleic Acid Atoms Solvent Atoms 130 Heterogen Atoms 14
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction