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Crystal structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with fragment-4 N10142 (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 2.16 43.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.808 α = 90 b = 91.958 β = 90 c = 24.091 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 2014-07-21 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 1.37 21.76 95.4 0.057 0.032 0.991 11.9 3.6 27767
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 1.37 1.43 91.4 0.524 0.303 0.649 2.2 3.6 2973
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 1.37 21.76 26322 1409 94.42 0.181 0.1789 0.178 0.2203 0.2332 RANDOM 27.512
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] 3.31 -2.35 -0.96
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 69.631 r_dihedral_angle_2_deg 28.378 r_sphericity_bonded 26.675 r_dihedral_angle_4_deg 12.637 r_dihedral_angle_3_deg 12.36 r_dihedral_angle_1_deg 5.184 r_mcangle_it 2.981 r_rigid_bond_restr 2.726 r_mcbond_it 2.621 r_mcbond_other 2.62
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 69.631 r_dihedral_angle_2_deg 28.378 r_sphericity_bonded 26.675 r_dihedral_angle_4_deg 12.637 r_dihedral_angle_3_deg 12.36 r_dihedral_angle_1_deg 5.184 r_mcangle_it 2.981 r_rigid_bond_restr 2.726 r_mcbond_it 2.621 r_mcbond_other 2.62 r_angle_refined_deg 1.724 r_angle_other_deg 1.102 r_chiral_restr 0.1 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.004 r_bond_other_d 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 996 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 20
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction