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Crystal structure of OphA-DeltaC6 mutant W400A in complex with Sinefungin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5N0O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289 0.3-0.4 M KSCN, 0.1 M Bicine pH 8.5, 1.3-1.5 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 3.55 65.31
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.54 α = 90 b = 91.94 β = 90 c = 162.01 γ = 90
Symmetry Space Group I 2 2 2
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 PILATUS3 6M 2017-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.7 Diamond I24
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.7 49.55 100 0.064 0.999 14.1 7.5 70395
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.73 100 1.73 0.47 1.2 7.7
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 5N0O 1.7 49.55 66862 3533 99.97 0.16639 0.16506 0.19155 0.2169 RANDOM 40.921
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] 0.33 0.83 -1.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.664 r_sphericity_free 29.905 r_dihedral_angle_4_deg 16.793 r_sphericity_bonded 12.328 r_dihedral_angle_3_deg 12.05 r_dihedral_angle_1_deg 5.946 r_long_range_B_refined 3.22 r_long_range_B_other 3.175 r_mcangle_it 2.395 r_mcangle_other 2.395
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.664 r_sphericity_free 29.905 r_dihedral_angle_4_deg 16.793 r_sphericity_bonded 12.328 r_dihedral_angle_3_deg 12.05 r_dihedral_angle_1_deg 5.946 r_long_range_B_refined 3.22 r_long_range_B_other 3.175 r_mcangle_it 2.395 r_mcangle_other 2.395 r_scangle_other 2.381 r_scbond_it 1.875 r_scbond_other 1.861 r_mcbond_it 1.73 r_mcbond_other 1.725 r_rigid_bond_restr 1.674 r_angle_refined_deg 1.374 r_angle_other_deg 0.926 r_chiral_restr 0.083 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3010 Nucleic Acid Atoms Solvent Atoms 183 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing