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Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0103080
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1TFF 1TFF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 16% PEG4K, 0.1M HEPES pH 7.0, 8% 2-propanol, 5 mM DTT
Crystal Properties Matthews coefficient Solvent content 2.33 47.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.21 α = 90 b = 58.41 β = 115.85 c = 49.58 γ = 90
Symmetry Space Group P 1 21 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 PILATUS 6M 2017-06-28 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.92819 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 1.63 44.62 99.6 0.094 0.112 0.06 0.997 8.5 3.3 30252
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 1.63 1.67 99.8 0.948 1.126 0.603 0.525 3.4 2225
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 1TFF 1.63 44.62 28903 1331 99.56 0.1793 0.1781 0.2056 0.1961 RANDOM 19.85
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] -0.01 -0.01 -0.01 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.371 r_dihedral_angle_4_deg 23.351 r_dihedral_angle_3_deg 12.488 r_dihedral_angle_1_deg 6.502 r_mcangle_it 2.286 r_angle_refined_deg 1.633 r_mcbond_it 1.54 r_mcbond_other 1.507 r_angle_other_deg 1.031 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.371 r_dihedral_angle_4_deg 23.351 r_dihedral_angle_3_deg 12.488 r_dihedral_angle_1_deg 6.502 r_mcangle_it 2.286 r_angle_refined_deg 1.633 r_mcbond_it 1.54 r_mcbond_other 1.507 r_angle_other_deg 1.031 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1847 Nucleic Acid Atoms Solvent Atoms 206 Heterogen Atoms 19
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing