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Crystal structure of OphA-DeltaC6 mutant W400A in complex with SAM
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 9.0, 1.7-1.9 M sodium malonate
Crystal Properties Matthews coefficient Solvent content 3.46 64.42
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.885 α = 90 b = 91.951 β = 90 c = 162.181 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 2017-01-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9763 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 1.59 75.9 98.6 0.045 0.997 14.9 7.3 85158
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 1.59 1.62 95.3 1.545 0.605 1.2 7.2
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 1.59 75.9 79834 4159 97.22 0.17411 0.17253 0.1841 0.20328 0.214 RANDOM 41.61
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] -1.32 -0.54 1.86
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.479 r_sphericity_free 30.381 r_dihedral_angle_4_deg 15.704 r_dihedral_angle_3_deg 12.725 r_sphericity_bonded 7.767 r_dihedral_angle_1_deg 6.17 r_long_range_B_refined 3.405 r_long_range_B_other 3.168 r_mcangle_it 2.421 r_mcangle_other 2.421
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.479 r_sphericity_free 30.381 r_dihedral_angle_4_deg 15.704 r_dihedral_angle_3_deg 12.725 r_sphericity_bonded 7.767 r_dihedral_angle_1_deg 6.17 r_long_range_B_refined 3.405 r_long_range_B_other 3.168 r_mcangle_it 2.421 r_mcangle_other 2.421 r_scangle_other 2.301 r_scbond_it 1.972 r_scbond_other 1.971 r_mcbond_it 1.969 r_mcbond_other 1.938 r_angle_refined_deg 1.329 r_rigid_bond_restr 1.011 r_angle_other_deg 0.93 r_chiral_restr 0.084 r_bond_refined_d 0.007 r_gen_planes_refined 0.005 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 3042 Nucleic Acid Atoms Solvent Atoms 235 Heterogen Atoms 56
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing