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Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102998
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 2.35 47.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.24 α = 90 b = 58.635 β = 116.18 c = 49.79 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 1.39 29.32 97.6 0.059 0.07 0.037 0.998 11.1 3.4 47767
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 1.39 1.43 95.3 0.603 0.751 0.439 0.643 2.8 3439
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 1TFF 1.39 29.33 45594 2152 97.31 0.1387 0.1365 0.1351 0.1838 0.1835 RANDOM 19.971
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] 0.66 0.28 -0.17 -0.52
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 30.532 r_dihedral_angle_2_deg 29.703 r_dihedral_angle_4_deg 23.299 r_sphericity_bonded 19.503 r_dihedral_angle_3_deg 12.049 r_dihedral_angle_1_deg 6.773 r_rigid_bond_restr 4.425 r_mcangle_it 3.263 r_mcbond_it 2.584 r_mcbond_other 2.582
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 30.532 r_dihedral_angle_2_deg 29.703 r_dihedral_angle_4_deg 23.299 r_sphericity_bonded 19.503 r_dihedral_angle_3_deg 12.049 r_dihedral_angle_1_deg 6.773 r_rigid_bond_restr 4.425 r_mcangle_it 3.263 r_mcbond_it 2.584 r_mcbond_other 2.582 r_angle_refined_deg 1.952 r_angle_other_deg 1.183 r_chiral_restr 0.1 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1843 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing