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Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0103007
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 2.37 48.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.554 α = 90 b = 58.334 β = 116.38 c = 50.333 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 29.17 98.4 0.074 0.088 0.047 0.997 9.1 3.3 48731
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 96.3 0.621 0.773 0.453 0.629 2.8 3505
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 29.18 46522 2189 98.13 0.1494 0.1471 0.1471 0.1978 0.1988 RANDOM 14.222
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] -0.04 -0.09 0.4 -0.18
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.912 r_dihedral_angle_2_deg 32.362 r_dihedral_angle_4_deg 19.625 r_sphericity_bonded 18.967 r_dihedral_angle_3_deg 12.544 r_rigid_bond_restr 12.475 r_dihedral_angle_1_deg 12.456 r_mcangle_it 2.819 r_mcbond_it 2.206 r_mcbond_other 2.205
RMS Deviations Key Refinement Restraint Deviation r_sphericity_free 32.912 r_dihedral_angle_2_deg 32.362 r_dihedral_angle_4_deg 19.625 r_sphericity_bonded 18.967 r_dihedral_angle_3_deg 12.544 r_rigid_bond_restr 12.475 r_dihedral_angle_1_deg 12.456 r_mcangle_it 2.819 r_mcbond_it 2.206 r_mcbond_other 2.205 r_angle_refined_deg 2.084 r_angle_other_deg 1.113 r_chiral_restr 0.103 r_bond_refined_d 0.02 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1820 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 44
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing