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Crystal Structure of the bromodomain of human BAZ2B in complex WITH GSK2801
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G0L
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277.15 28% Low Molecular-Weight PEG Smears, 0.1M MES pH 6.5 (Ligand soaking performed in low-molecular-weight PEG smears stabilizing solution) , VAPOR DIFFUSION, SITTING DROP, temperature 277.15K
Crystal Properties Matthews coefficient Solvent content 4.27 71.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.72 α = 90 b = 96.975 β = 90 c = 58.06 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS IV 2012-03-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU FR-E SUPERBRIGHT 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.98 31.43 100 0.062 13.5 5 16635 16611 39.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.98 2.09 100 0.647 2.1 5 2385
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3G0L 1.98 30.11 2 16611 15770 841 99.8 0.18915 0.18686 0.1917 0.23196 0.2327 RANDOM 44.683
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] 1.21 0.08 -1.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.634 r_dihedral_angle_4_deg 16.825 r_dihedral_angle_3_deg 13.474 r_long_range_B_refined 12.494 r_long_range_B_other 12.491 r_scangle_other 10.503 r_scbond_it 7.99 r_scbond_other 7.985 r_mcangle_it 7.972 r_mcangle_other 7.967
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.634 r_dihedral_angle_4_deg 16.825 r_dihedral_angle_3_deg 13.474 r_long_range_B_refined 12.494 r_long_range_B_other 12.491 r_scangle_other 10.503 r_scbond_it 7.99 r_scbond_other 7.985 r_mcangle_it 7.972 r_mcangle_other 7.967 r_mcbond_it 6.122 r_dihedral_angle_1_deg 6.063 r_mcbond_other 6.051 r_angle_refined_deg 1.505 r_angle_other_deg 0.741 r_chiral_restr 0.083 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 948 Nucleic Acid Atoms Solvent Atoms 176 Heterogen Atoms 50
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling