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PanDDA analysis group deposition -- Crystal Structure of BRD1 after initial refinement with no ligand modelled (structure 65)
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 2.16 43.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 55.023 α = 90 b = 56.29 β = 90 c = 101.811 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 1.82 29.06 98.8 0.071 0.078 0.03 0.999 19.4 6.6 28841
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 1.82 1.86 96 0.796 0.864 0.332 0.822 6.5 2020
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT 5AMF 1.82 29.06 27445 1350 98.42 0.1858 0.1843 0.1925 0.2171 0.2222 RANDOM 27.911
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] 2.39 -0.93 -1.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.069 r_dihedral_angle_4_deg 17.497 r_dihedral_angle_3_deg 13.466 r_dihedral_angle_1_deg 4.945 r_mcangle_it 3.559 r_mcbond_it 2.639 r_mcbond_other 2.624 r_angle_refined_deg 1.776 r_angle_other_deg 1.087 r_chiral_restr 0.111
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.069 r_dihedral_angle_4_deg 17.497 r_dihedral_angle_3_deg 13.466 r_dihedral_angle_1_deg 4.945 r_mcangle_it 3.559 r_mcbond_it 2.639 r_mcbond_other 2.624 r_angle_refined_deg 1.776 r_angle_other_deg 1.087 r_chiral_restr 0.111 r_bond_refined_d 0.019 r_gen_planes_refined 0.008 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