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Crystal structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with N-(2,6-Dichlorobenzyl)acetamide (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 2.14 42.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.687 α = 90 b = 91.582 β = 90 c = 24.033 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 2014-10-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92001 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 1.59 28.8 99.8 0.041 0.018 0.999 21.8 6.4 18820
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 1.59 1.63 98.7 0.726 0.314 0.791 2.4 6.2 1343
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 1.59 28.8 17845 933 99.71 0.2057 0.2035 0.2114 0.2466 0.2548 RANDOM 31.014
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] -1.16 1.65 -0.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.796 r_dihedral_angle_3_deg 12.982 r_dihedral_angle_4_deg 10.797 r_dihedral_angle_1_deg 6.237 r_mcangle_it 2.086 r_angle_refined_deg 1.662 r_mcbond_it 1.34 r_mcbond_other 1.339 r_angle_other_deg 1.024 r_chiral_restr 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.796 r_dihedral_angle_3_deg 12.982 r_dihedral_angle_4_deg 10.797 r_dihedral_angle_1_deg 6.237 r_mcangle_it 2.086 r_angle_refined_deg 1.662 r_mcbond_it 1.34 r_mcbond_other 1.339 r_angle_other_deg 1.024 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1018 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 21
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction