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Crystal structure of CapF with inhibitor 3-isopropenyl-tropolone
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ST7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 298 Sodium cacodylate 100mM, Potassium phosphate 200mM, PEG 3350 18%
Crystal Properties Matthews coefficient Solvent content 3.7 66.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.58 α = 90 b = 194.62 β = 90 c = 158.36 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315 2014-12-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.44 52.8 93.4 0.129 8.8 6.1 42336
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.44 2.57 89 0.576 2.8 5.9
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 MOLECULAR REPLACEMENT THROUGHOUT 3ST7 2.44 52.8 40164 2139 92.85 0.23102 0.22938 0.26091 0.2454 RANDOM 31.251
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] 0.61 -1.06 0.46
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.504 r_dihedral_angle_4_deg 20.347 r_dihedral_angle_3_deg 15.208 r_dihedral_angle_1_deg 6.338 r_long_range_B_refined 3.736 r_long_range_B_other 3.635 r_scangle_other 1.856 r_angle_refined_deg 1.63 r_mcangle_it 1.531 r_mcangle_other 1.531
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.504 r_dihedral_angle_4_deg 20.347 r_dihedral_angle_3_deg 15.208 r_dihedral_angle_1_deg 6.338 r_long_range_B_refined 3.736 r_long_range_B_other 3.635 r_scangle_other 1.856 r_angle_refined_deg 1.63 r_mcangle_it 1.531 r_mcangle_other 1.531 r_scbond_it 1.08 r_scbond_other 1.08 r_angle_other_deg 0.991 r_mcbond_it 0.88 r_mcbond_other 0.88 r_chiral_restr 0.096 r_bond_refined_d 0.013 r_gen_planes_refined 0.007 r_bond_other_d 0.003 r_gen_planes_other 0.003 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5560 Nucleic Acid Atoms Solvent Atoms 194 Heterogen Atoms 26
Software Software Software Name Purpose REFMAC refinement