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Crystal structure of OphA-DeltaC6 mutant Y98A 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 3.6 65.85
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 163.906 α = 90 b = 92.521 β = 90 c = 85.332 γ = 90
Symmetry Space Group P 21 21 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 CCD RIGAKU SATURN 944+ 2016-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
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 1.95 85.33 98.4 0.098 0.996 6.7 5.9 93739
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 1.95 2.09 95.1 1.017 0.657 1 4.5
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 THROUGHOUT 5N0o 1.95 85.33 88960 4632 98.33 0.20663 0.20526 0.211 0.23335 0.2379 RANDOM 44.812
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] 1.7 -0.67 -1.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.361 r_dihedral_angle_4_deg 16.893 r_dihedral_angle_3_deg 12.948 r_dihedral_angle_1_deg 6.079 r_long_range_B_other 5.543 r_long_range_B_refined 5.542 r_mcangle_it 2.376 r_mcangle_other 2.376 r_scangle_other 2.197 r_angle_refined_deg 1.439
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.361 r_dihedral_angle_4_deg 16.893 r_dihedral_angle_3_deg 12.948 r_dihedral_angle_1_deg 6.079 r_long_range_B_other 5.543 r_long_range_B_refined 5.542 r_mcangle_it 2.376 r_mcangle_other 2.376 r_scangle_other 2.197 r_angle_refined_deg 1.439 r_mcbond_it 1.367 r_mcbond_other 1.367 r_scbond_it 1.299 r_scbond_other 1.296 r_angle_other_deg 0.938 r_chiral_restr 0.081 r_bond_refined_d 0.009 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 6215 Nucleic Acid Atoms Solvent Atoms 524 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction Aimless data scaling PHASER phasing