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XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with E07179c (space group P212121)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3MB3 3MB3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 0.1M HEPES pH 7.5 -- 0.1M calcium chloride -- 10% ethylene glycol -- 12% PEG6K
Crystal Properties Matthews coefficient Solvent content 2.03 39.27
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.29 α = 90 b = 57.32 β = 90 c = 90.6 γ = 90
Symmetry Space Group P 21 21 21
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 2017-10-03 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9795 Diamond I04
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 1.41 47.29 99.5 0.054 0.059 0.022 1 16.4 7.1 48052
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 1.41 1.45 94.7 1.485 1.635 0.667 0.473 5.7 3332
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 3MB3 1.41 41.96 45652 2335 99.43 0.1629 0.1606 0.2051 0.2062 RANDOM 22.329
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] 1.26 -0.96 -0.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.379 r_dihedral_angle_4_deg 15.293 r_dihedral_angle_3_deg 14.033 r_dihedral_angle_1_deg 5.315 r_rigid_bond_restr 2.814 r_mcangle_it 2.504 r_mcbond_it 2.254 r_mcbond_other 2.166 r_angle_refined_deg 1.651 r_angle_other_deg 1.585
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.379 r_dihedral_angle_4_deg 15.293 r_dihedral_angle_3_deg 14.033 r_dihedral_angle_1_deg 5.315 r_rigid_bond_restr 2.814 r_mcangle_it 2.504 r_mcbond_it 2.254 r_mcbond_other 2.166 r_angle_refined_deg 1.651 r_angle_other_deg 1.585 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1979 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing