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Crystal structure of bromodomain from Plasmodium falciparum GCN5 complexed with a ligand
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5TPX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.2 291 Protein: 22.6 mg/mL in 20 mM HEPES, 150 mM NaCl, 0.5 mM TCEP, pH 7.5, 3.6 mM compound.
Reservoir: 0.2 M sodium chloride, 0.1 M phosphate/citrate pH 4.2, 20% w/v PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.28 46.12
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 58.079 α = 90 b = 165.488 β = 90 c = 35.974 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 EIGER X 16M 2025-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.9537 Diamond I04
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 1.8 55.16 100 0.158 0.064 0.998 9.5 13 33196
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.84 99.9 2.12 0.92 0.605 12
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 1.8 54.86 31506 1623 99.98 0.20049 0.19829 0.2073 0.24584 0.2566 RANDOM 33.903
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] -0.52 -0.41 0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.119 r_dihedral_angle_2_deg 8.747 r_long_range_B_refined 5.561 r_long_range_B_other 5.506 r_dihedral_angle_1_deg 5.161 r_scangle_other 3.072 r_scbond_it 1.888 r_scbond_other 1.888 r_mcangle_other 1.683 r_mcangle_it 1.682
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 13.119 r_dihedral_angle_2_deg 8.747 r_long_range_B_refined 5.561 r_long_range_B_other 5.506 r_dihedral_angle_1_deg 5.161 r_scangle_other 3.072 r_scbond_it 1.888 r_scbond_other 1.888 r_mcangle_other 1.683 r_mcangle_it 1.682 r_angle_refined_deg 1.644 r_mcbond_it 1.123 r_mcbond_other 1.123 r_angle_other_deg 0.58 r_chiral_restr 0.091 r_bond_refined_d 0.008 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2633 Nucleic Acid Atoms Solvent Atoms 229 Heterogen Atoms 85
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DIALS data reduction Aimless data scaling MOLREP phasing Coot model building