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Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with P11
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 2.28 46.09
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.797 α = 90 b = 58.146 β = 116.25 c = 49.295 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 2018-01-18 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.91587 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 29.07 98.5 0.04 0.048 0.026 0.999 14.3 3 40667
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 92.7 0.357 0.475 0.31 0.85 2.1 2809
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 29.09 38873 1769 98.34 0.1736 0.1725 0.1974 0.2126 RANDOM 18.261
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] -0.02 0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.758 r_dihedral_angle_4_deg 23.655 r_dihedral_angle_3_deg 12.462 r_dihedral_angle_1_deg 6.809 r_mcangle_it 2.436 r_angle_other_deg 2.103 r_angle_refined_deg 1.735 r_mcbond_it 1.591 r_mcbond_other 1.534 r_chiral_restr 0.087
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.758 r_dihedral_angle_4_deg 23.655 r_dihedral_angle_3_deg 12.462 r_dihedral_angle_1_deg 6.809 r_mcangle_it 2.436 r_angle_other_deg 2.103 r_angle_refined_deg 1.735 r_mcbond_it 1.591 r_mcbond_other 1.534 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.01 r_gen_planes_other 0.008 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1847 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 24
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing