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Crystal structure of OphA-DeltaC6 mutant Y66F 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, 1.5-1.9 M sodium malonate and 0.1 M bicine pH 9.0
Crystal Properties Matthews coefficient Solvent content 3.72 66.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.652 α = 90 b = 93.355 β = 90 c = 165.355 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 PILATUS 6M-F 2016-09-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04-1 0.9281 Diamond I04-1
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 1.61 82.68 98 0.025 1 27.6 5.5 84772
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 1.61 1.64 98 0.609 0.842
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 1.61 82.68 80525 4197 98 0.1783 0.1776 0.19124 0.2152 RANDOM 38.849
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] -0.54 -0.51 1.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.566 r_dihedral_angle_4_deg 14.767 r_dihedral_angle_3_deg 11.891 r_dihedral_angle_1_deg 5.591 r_long_range_B_refined 4.535 r_long_range_B_other 4.297 r_scangle_other 1.793 r_mcangle_it 1.761 r_mcangle_other 1.761 r_angle_refined_deg 1.34
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.566 r_dihedral_angle_4_deg 14.767 r_dihedral_angle_3_deg 11.891 r_dihedral_angle_1_deg 5.591 r_long_range_B_refined 4.535 r_long_range_B_other 4.297 r_scangle_other 1.793 r_mcangle_it 1.761 r_mcangle_other 1.761 r_angle_refined_deg 1.34 r_scbond_it 1.098 r_scbond_other 1.098 r_mcbond_it 1.001 r_mcbond_other 1.001 r_angle_other_deg 0.913 r_chiral_restr 0.08 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.001 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 3004 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 49
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing