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Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in space group C2
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 277 20% PEG8000, 0.04M potassium phosphate monobasic
Crystal Properties Matthews coefficient Solvent content 2 38.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.49 α = 90 b = 27.02 β = 100.5 c = 55.94 γ = 90
Symmetry Space Group C 1 2 1
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 1.23 14.51 96.9 0.997 22.9 2.9 34009
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 1.23 1.25 0.987
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3MB3 1.23 14.51 34009 1635 96.531 0.119 0.1179 0.1133 0.146 0.1464 14.779
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] -0.293 -0.597 2.821 -2.158
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.364 r_dihedral_angle_3_deg 11.717 r_dihedral_angle_4_deg 10.94 r_dihedral_angle_1_deg 5.506 r_rigid_bond_restr 4.503 r_lrange_it 4.078 r_lrange_other 3.54 r_scangle_it 3.369 r_scangle_other 3.367 r_scbond_it 2.817
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.364 r_dihedral_angle_3_deg 11.717 r_dihedral_angle_4_deg 10.94 r_dihedral_angle_1_deg 5.506 r_rigid_bond_restr 4.503 r_lrange_it 4.078 r_lrange_other 3.54 r_scangle_it 3.369 r_scangle_other 3.367 r_scbond_it 2.817 r_scbond_other 2.815 r_mcangle_other 2.055 r_mcangle_it 2 r_mcbond_it 1.895 r_angle_refined_deg 1.885 r_angle_other_deg 1.72 r_mcbond_other 1.623 r_nbd_refined 0.25 r_nbd_other 0.204 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.195 r_symmetry_xyhbond_nbd_refined 0.185 r_xyhbond_nbd_refined 0.169 r_symmetry_nbd_refined 0.165 r_chiral_restr 0.117 r_symmetry_nbtor_other 0.089 r_xyhbond_nbd_other 0.076 r_bond_refined_d 0.015 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1025 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing