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Crystal structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with 5-Amino-2-benzyl-1,3-oxazole-4-carbonitrile (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 2.15 42.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.549 α = 90 b = 91.936 β = 90 c = 24.082 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 0.9200 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 1.49 28.76 99.4 0.036 0.016 0.999 23.3 6.4 22778
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 1.49 1.53 99 0.703 0.295 0.896 2.3 6.5 1641
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 1.49 28.76 21578 1152 99.12 0.2047 0.203 0.212 0.2379 0.2461 RANDOM 30.205
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] -1.61 1 0.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.559 r_dihedral_angle_3_deg 12.392 r_dihedral_angle_4_deg 9.91 r_dihedral_angle_1_deg 5.263 r_mcangle_it 1.848 r_angle_refined_deg 1.573 r_mcbond_it 1.175 r_mcbond_other 1.174 r_angle_other_deg 0.973 r_chiral_restr 0.096
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.559 r_dihedral_angle_3_deg 12.392 r_dihedral_angle_4_deg 9.91 r_dihedral_angle_1_deg 5.263 r_mcangle_it 1.848 r_angle_refined_deg 1.573 r_mcbond_it 1.175 r_mcbond_other 1.174 r_angle_other_deg 0.973 r_chiral_restr 0.096 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1006 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 15
Software Software Software Name Purpose Aimless data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction