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Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in complex with H4K5acK8ac
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 8.5 277 30% 2-propanol -- 0.2M ammonium acetate -- 0.1M tris pH 8.5
Crystal Properties Matthews coefficient Solvent content 2.45 49.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.21 α = 90 b = 58.31 β = 99.08 c = 77.12 γ = 90
Symmetry Space Group P 1 21 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 2016-06-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9282 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 1.99 55.39 99 0.998 11.3 3.4 41404
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 1.99 2.04 0.653
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 1.99 55.39 41394 2016 98.858 0.207 0.2055 0.2138 0.2405 0.2434 38.966
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] -0.279 0.545 1.134 -0.978
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.139 r_dihedral_angle_4_deg 15.872 r_dihedral_angle_3_deg 14.492 r_lrange_other 7.575 r_lrange_it 7.564 r_scangle_it 5.999 r_scangle_other 5.998 r_dihedral_angle_1_deg 5.272 r_mcangle_other 4.634 r_mcangle_it 4.63
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.139 r_dihedral_angle_4_deg 15.872 r_dihedral_angle_3_deg 14.492 r_lrange_other 7.575 r_lrange_it 7.564 r_scangle_it 5.999 r_scangle_other 5.998 r_dihedral_angle_1_deg 5.272 r_mcangle_other 4.634 r_mcangle_it 4.63 r_scbond_it 3.889 r_scbond_other 3.888 r_mcbond_it 3.269 r_mcbond_other 3.229 r_angle_refined_deg 1.456 r_angle_other_deg 1.305 r_nbd_refined 0.203 r_nbd_other 0.187 r_nbtor_refined 0.163 r_symmetry_nbd_other 0.159 r_xyhbond_nbd_refined 0.15 r_symmetry_xyhbond_nbd_refined 0.133 r_symmetry_nbd_refined 0.127 r_ncsr_local_group_3 0.092 r_ncsr_local_group_4 0.092 r_ncsr_local_group_6 0.092 r_ncsr_local_group_1 0.083 r_ncsr_local_group_2 0.083 r_chiral_restr 0.078 r_symmetry_nbtor_other 0.077 r_ncsr_local_group_5 0.075 r_bond_refined_d 0.008 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 4031 Nucleic Acid Atoms Solvent Atoms 165 Heterogen Atoms 12
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing