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High resolution structure of BRPF1 Bromo Domain from Biortus
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EWC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.2 M Potassium fluoride, 20 %(w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.01 38.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.601 α = 90 b = 60.601 β = 90 c = 59.169 γ = 120
Symmetry Space Group P 32 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 EIGER X 16M 2020-04-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS-II BEAMLINE 17-ID-2 0.97936 NSLS-II 17-ID-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.37 39.293 100 0.074 0.998 12.3 7.8 26865
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 1.37 1.39 0.797
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 5ewc 1.37 39.293 26832 1367 99.944 0.168 0.1663 0.1689 0.1937 0.1977 20.364
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] -0.552 -0.276 -0.552 1.792
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.25 r_dihedral_angle_4_deg 22.408 r_dihedral_angle_3_deg 12.019 r_lrange_it 5.896 r_lrange_other 5.751 r_dihedral_angle_1_deg 4.881 r_scangle_it 3.347 r_scangle_other 3.345 r_scbond_it 2.136 r_scbond_other 2.134
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.25 r_dihedral_angle_4_deg 22.408 r_dihedral_angle_3_deg 12.019 r_lrange_it 5.896 r_lrange_other 5.751 r_dihedral_angle_1_deg 4.881 r_scangle_it 3.347 r_scangle_other 3.345 r_scbond_it 2.136 r_scbond_other 2.134 r_mcangle_other 1.485 r_mcangle_it 1.484 r_angle_other_deg 1.412 r_angle_refined_deg 1.356 r_mcbond_it 1.03 r_mcbond_other 1.028 r_nbd_refined 0.274 r_nbd_other 0.236 r_symmetry_nbd_other 0.206 r_symmetry_nbd_refined 0.196 r_metal_ion_refined 0.183 r_nbtor_refined 0.172 r_xyhbond_nbd_refined 0.131 r_symmetry_xyhbond_nbd_refined 0.13 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.072 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 960 Nucleic Acid Atoms Solvent Atoms 151 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing