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Crystal structure of human SP100 PHD-Bromodomain in the free state
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 277 22% PEG 20000, 0.1M MES pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.72 54.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.52 α = 90 b = 45.183 β = 102.21 c = 83.188 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 6M 2013-12-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 1.282 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 1.6 28.37 100 0.045 0.028 23.3 6.7 58158 58158 19.26
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.6 1.69 100 0.291 0.291 4.65 3.45 17539
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 SAD THROUGHOUT 1.6 27.72 55205 55205 2950 94.17 0.17402 0.17402 0.17303 0.1858 0.19229 0.2022 RANDOM 25.806
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] -0.6 0.38 -0.3 0.67
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.802 r_dihedral_angle_4_deg 14.49 r_dihedral_angle_3_deg 12.542 r_long_range_B_refined 5.732 r_long_range_B_other 5.689 r_dihedral_angle_1_deg 5.27 r_scangle_other 4.127 r_scbond_it 2.59 r_scbond_other 2.589 r_mcangle_other 2.505
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.802 r_dihedral_angle_4_deg 14.49 r_dihedral_angle_3_deg 12.542 r_long_range_B_refined 5.732 r_long_range_B_other 5.689 r_dihedral_angle_1_deg 5.27 r_scangle_other 4.127 r_scbond_it 2.59 r_scbond_other 2.589 r_mcangle_other 2.505 r_mcangle_it 2.504 r_mcbond_it 1.564 r_mcbond_other 1.556 r_angle_refined_deg 1.392 r_angle_other_deg 0.804 r_chiral_restr 0.083 r_bond_refined_d 0.011 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 2866 Nucleic Acid Atoms Solvent Atoms 200 Heterogen Atoms 32
Software Software Software Name Purpose ADSC data collection SHELXS phasing REFMAC refinement XDS data reduction SCALA data scaling