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Crystal structure of the bromodomain from Plasmodium falciparum bromodomain protein 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5ULC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 277 0.3 M lithium sulfate, 0.1 M tris, pH 8.5, 38% PEG400
Crystal Properties Matthews coefficient Solvent content 3.13 60.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.051 α = 90 b = 88.667 β = 90 c = 106.797 γ = 90
Symmetry Space Group I 2 2 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 CMOS RDI CMOS_8M 2020-07-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.9762 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 2 35.84 99.63 0.02602 0.0368 0.02602 0.999 19.24 2 12597 29.39
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2 2.072 0.2672 0.3779 0.2672 0.93 2.93
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5ulc 2 35.84 1.34 12572 587 99.66 0.1958 0.1939 0.1984 0.2347 0.2371 46.01
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 20.7945 f_angle_d 0.8887 f_chiral_restr 0.0541 f_bond_d 0.0082 f_plane_restr 0.0041
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 989 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement PHASER phasing XDS data scaling XDS data reduction Coot model building