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PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 12)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5AMF 5AMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1M bis-tris pH 7.0 -- 30% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.14 42.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.793 α = 90 b = 56.128 β = 90 c = 101.48 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 2M 2014-08-28 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9200 Diamond I04-1
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 1.61 28.97 99.5 0.048 0.052 0.02 1 24 6.5 41282
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 1.61 1.65 97.3 0.828 0.911 0.373 0.783 5.7 2903
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5AMF 1.61 28.97 39183 2042 99.34 0.1795 0.1778 0.2126 0.2079 RANDOM 25.282
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] 1.88 -0.88 -1.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.79 r_dihedral_angle_4_deg 14.505 r_dihedral_angle_3_deg 13.273 r_dihedral_angle_1_deg 4.681 r_mcangle_it 3.108 r_mcbond_it 2.348 r_mcbond_other 2.342 r_angle_refined_deg 1.954 r_angle_other_deg 1.104 r_chiral_restr 0.126
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.79 r_dihedral_angle_4_deg 14.505 r_dihedral_angle_3_deg 13.273 r_dihedral_angle_1_deg 4.681 r_mcangle_it 3.108 r_mcbond_it 2.348 r_mcbond_other 2.342 r_angle_refined_deg 1.954 r_angle_other_deg 1.104 r_chiral_restr 0.126 r_bond_refined_d 0.022 r_gen_planes_refined 0.01 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1953 Nucleic Acid Atoms Solvent Atoms 259 Heterogen Atoms 21
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing