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full length OphA V404E in complex with SAH
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, 1.8-2.3 M Sodium malonate
Crystal Properties Matthews coefficient Solvent content 3.7 66.77
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 164.002 α = 90 b = 91.723 β = 90 c = 85.222 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 PIXEL DECTRIS PILATUS3 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 1.85 80.1 100 0.044 1 16.9 7.2 798741 110277
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 1.85 1.88 98.4 0.766 0.621 2 7.3
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 1.85 80.05 104622 5568 99.9 0.20731 0.20638 0.2154 0.22462 0.2339 RANDOM 50.04
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] 0.75 -0.91 0.16
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.06 r_dihedral_angle_4_deg 16.221 r_dihedral_angle_3_deg 13.355 r_long_range_B_refined 9.723 r_long_range_B_other 9.723 r_scangle_other 7.929 r_dihedral_angle_1_deg 6.783 r_scbond_it 5.867 r_scbond_other 5.867 r_mcangle_it 5.382
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.06 r_dihedral_angle_4_deg 16.221 r_dihedral_angle_3_deg 13.355 r_long_range_B_refined 9.723 r_long_range_B_other 9.723 r_scangle_other 7.929 r_dihedral_angle_1_deg 6.783 r_scbond_it 5.867 r_scbond_other 5.867 r_mcangle_it 5.382 r_mcangle_other 5.382 r_mcbond_it 4.41 r_mcbond_other 4.41 r_angle_refined_deg 1.393 r_angle_other_deg 1.27 r_chiral_restr 0.063 r_bond_refined_d 0.007 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 6083 Nucleic Acid Atoms Solvent Atoms 326 Heterogen Atoms 52
Software Software Software Name Purpose REFMAC refinement DIALS data reduction DIALS data scaling PHASER phasing