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Covalent fragment group deposition -- Crystal Structure of OUTB2 in complex with PCM-0103011
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 2.36 47.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 47.444 α = 90 b = 58.427 β = 116.28 c = 50.14 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 1.56 29.21 99.8 0.078 0.092 0.049 0.998 9.9 3.4 34960
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 1.56 1.6 98.9 0.702 0.832 0.442 0.646 3.4 2535
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 1.56 29.23 33393 1535 99.76 0.1477 0.1447 0.1594 0.2106 0.2191 RANDOM 21.006
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] 0.11 0.02 -0.15 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.902 r_sphericity_free 29.247 r_dihedral_angle_4_deg 23.566 r_sphericity_bonded 16.822 r_dihedral_angle_3_deg 13.323 r_dihedral_angle_1_deg 6.401 r_mcangle_it 3.732 r_mcbond_it 2.884 r_mcbond_other 2.837 r_rigid_bond_restr 2.811
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.902 r_sphericity_free 29.247 r_dihedral_angle_4_deg 23.566 r_sphericity_bonded 16.822 r_dihedral_angle_3_deg 13.323 r_dihedral_angle_1_deg 6.401 r_mcangle_it 3.732 r_mcbond_it 2.884 r_mcbond_other 2.837 r_rigid_bond_restr 2.811 r_angle_other_deg 2.033 r_angle_refined_deg 1.773 r_chiral_restr 0.19 r_bond_refined_d 0.015 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1843 Nucleic Acid Atoms Solvent Atoms 234 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction XDS data reduction REFMAC phasing