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Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0102821
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 2.34 47.54
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.289 α = 90 b = 58.436 β = 115.87 c = 49.713 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 1.46 29.22 97.6 0.071 0.084 0.045 0.998 10.2 3.4 41348
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 1.46 1.5 95.2 0.677 0.818 0.452 0.65 3.2 2978
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 1.46 29.24 39512 1813 97.38 0.1439 0.1415 0.1946 0.2046 RANDOM 17.96
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] 0.31 -0.04 -0.19
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.588 r_sphericity_free 27.478 r_dihedral_angle_4_deg 21.424 r_sphericity_bonded 14.108 r_dihedral_angle_3_deg 12.284 r_dihedral_angle_1_deg 7.168 r_rigid_bond_restr 3.317 r_mcangle_it 3.223 r_mcbond_it 2.571 r_mcbond_other 2.522
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.588 r_sphericity_free 27.478 r_dihedral_angle_4_deg 21.424 r_sphericity_bonded 14.108 r_dihedral_angle_3_deg 12.284 r_dihedral_angle_1_deg 7.168 r_rigid_bond_restr 3.317 r_mcangle_it 3.223 r_mcbond_it 2.571 r_mcbond_other 2.522 r_angle_refined_deg 2.202 r_angle_other_deg 2.036 r_chiral_restr 0.095 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1843 Nucleic Acid Atoms Solvent Atoms 207 Heterogen Atoms 31
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing