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XChem group deposition -- Crystal Structure of the second bromodomain of pleckstrin homology domain interacting protein (PHIP) in complex with N01460c (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 -- 17% PEG6K
Crystal Properties Matthews coefficient Solvent content 2.04 39.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.57 α = 90 b = 57.17 β = 90 c = 91.14 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 1.67 45.57 99.9 0.075 0.08 0.03 0.999 14.8 7.2 29591
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 1.67 1.71 99.9 1.59 1.715 0.636 0.556 7 2165
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 1.67 45.57 28057 1480 99.84 0.2171 0.2155 0.2454 0.2292 RANDOM 26.384
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] 0.87 -0.8 -0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.532 r_dihedral_angle_3_deg 14.36 r_dihedral_angle_4_deg 11.259 r_dihedral_angle_1_deg 5.595 r_mcangle_it 2.713 r_mcbond_it 1.853 r_mcbond_other 1.844 r_angle_refined_deg 1.377 r_angle_other_deg 1.366 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.532 r_dihedral_angle_3_deg 14.36 r_dihedral_angle_4_deg 11.259 r_dihedral_angle_1_deg 5.595 r_mcangle_it 2.713 r_mcbond_it 1.853 r_mcbond_other 1.844 r_angle_refined_deg 1.377 r_angle_other_deg 1.366 r_chiral_restr 0.074 r_bond_refined_d 0.007 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 1973 Nucleic Acid Atoms Solvent Atoms 166 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing