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OphA Y63F-sinefungin complex
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 8-9, 1.7-2.0 M Sodium malonate
Crystal Properties Matthews coefficient Solvent content 4.06 69.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.784 α = 90 b = 89.784 β = 90 c = 156.902 γ = 120
Symmetry Space Group P 32 2 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 PILATUS3 S 6M 2018-04-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9686 Diamond I03
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 2.1 77.76 100 0.073 0.999 12.3 10.8 43488
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 2.1 2.14 98.64 1.017 0.556 2.1 11
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 MOLECULAR REPLACEMENT THROUGHOUT 5N0O 2.1 77.76 41277 2158 99.93 0.23602 0.2349 0.2383 0.2581 0.259 RANDOM 90.275
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] 0.47 0.24 0.47 -1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.666 r_dihedral_angle_4_deg 19.101 r_dihedral_angle_3_deg 15.331 r_dihedral_angle_1_deg 6.101 r_long_range_B_refined 3.513 r_long_range_B_other 3.51 r_mcangle_it 1.684 r_mcangle_other 1.684 r_scangle_other 1.362 r_angle_refined_deg 1.097
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.666 r_dihedral_angle_4_deg 19.101 r_dihedral_angle_3_deg 15.331 r_dihedral_angle_1_deg 6.101 r_long_range_B_refined 3.513 r_long_range_B_other 3.51 r_mcangle_it 1.684 r_mcangle_other 1.684 r_scangle_other 1.362 r_angle_refined_deg 1.097 r_mcbond_it 0.955 r_mcbond_other 0.955 r_scbond_it 0.765 r_scbond_other 0.764 r_angle_other_deg 0.402 r_chiral_restr 0.048 r_bond_refined_d 0.008 r_gen_planes_refined 0.006 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 r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2929 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms 53
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing