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Crystal Structure of the second bromodomain of Pleckstrin homology domain interacting protein (PHIP) in space group P21212
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 0.1M HEPES pH 7.5, 0.15M magnesium chloride, 32% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.2 44.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.62 α = 90 b = 91.81 β = 90 c = 23.98 γ = 90
Symmetry Space Group P 21 21 2
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 2014-03-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 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 1.63 50.59 99.7 0.999 27.5 6.3 17450
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 1.63 1.67 0.861
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 1.63 50.588 17405 880 99.531 0.209 0.207 0.2482 0.2775 36.407
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] -1.631 1.524 0.107
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.842 r_dihedral_angle_3_deg 14.504 r_dihedral_angle_4_deg 13.672 r_dihedral_angle_1_deg 5.435 r_lrange_it 5.112 r_lrange_other 5.065 r_scangle_it 3.373 r_scangle_other 3.371 r_mcangle_it 2.271 r_mcangle_other 2.271
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.842 r_dihedral_angle_3_deg 14.504 r_dihedral_angle_4_deg 13.672 r_dihedral_angle_1_deg 5.435 r_lrange_it 5.112 r_lrange_other 5.065 r_scangle_it 3.373 r_scangle_other 3.371 r_mcangle_it 2.271 r_mcangle_other 2.271 r_scbond_it 2.253 r_scbond_other 2.251 r_angle_refined_deg 1.502 r_mcbond_it 1.485 r_mcbond_other 1.48 r_angle_other_deg 1.453 r_nbd_refined 0.219 r_nbd_other 0.208 r_symmetry_xyhbond_nbd_refined 0.187 r_nbtor_refined 0.173 r_symmetry_nbd_other 0.163 r_xyhbond_nbd_refined 0.124 r_symmetry_nbd_refined 0.083 r_chiral_restr 0.08 r_symmetry_nbtor_other 0.077 r_xyhbond_nbd_other 0.019 r_bond_refined_d 0.009 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1014 Nucleic Acid Atoms Solvent Atoms 93 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement xia2 data reduction Aimless data scaling PHASER phasing