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Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in space group P212121
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 20% PEG6000 -- 10% ethylene glycol -- 0.1M tris pH 7.5 -- 0.1M calcium chloride
Crystal Properties Matthews coefficient Solvent content 2.04 39.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.726 α = 90 b = 56.477 β = 90 c = 91.79 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 2M 2015-04-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9173 Diamond I04-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.32 56.48 99.9 0.999 11.1 6 59052
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.37 0.577
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3MB3 1.32 48.148 58868 2843 99.71 0.188 0.1859 0.2255 0.2173 21.669
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] 2.64 -1.903 -0.737
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.54 r_dihedral_angle_4_deg 14.148 r_dihedral_angle_3_deg 12.728 r_rigid_bond_restr 6.557 r_dihedral_angle_1_deg 5.592 r_lrange_it 4.295 r_lrange_other 4.222 r_scangle_it 4.208 r_scangle_other 4.207 r_scbond_it 3.261
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 25.54 r_dihedral_angle_4_deg 14.148 r_dihedral_angle_3_deg 12.728 r_rigid_bond_restr 6.557 r_dihedral_angle_1_deg 5.592 r_lrange_it 4.295 r_lrange_other 4.222 r_scangle_it 4.208 r_scangle_other 4.207 r_scbond_it 3.261 r_scbond_other 3.261 r_mcangle_other 3.018 r_mcangle_it 3.015 r_mcbond_other 2.354 r_mcbond_it 2.347 r_angle_other_deg 1.677 r_angle_refined_deg 1.652 r_nbd_refined 0.222 r_nbd_other 0.21 r_symmetry_nbd_other 0.202 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.183 r_symmetry_nbd_refined 0.165 r_symmetry_xyhbond_nbd_refined 0.126 r_chiral_restr 0.098 r_metal_ion_refined 0.096 r_symmetry_nbtor_other 0.076 r_bond_other_d 0.014 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2032 Nucleic Acid Atoms Solvent Atoms 196 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement DIALS data reduction Aimless data scaling PHASER phasing