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Crystal structure of OphA-DeltaC18 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, SITTING DROP 289 0.04 M ammonium citrate tribasic, 0.1 M sodium citrate pH 5.5 and 27% PEG MME 5000.
Crystal Properties Matthews coefficient Solvent content 2.79 55.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.802 α = 90 b = 100.216 β = 90 c = 124.49 γ = 90
Symmetry Space Group P 21 21 21
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 2016-08-01 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 2.157 100.2 99.9 0.033 1 20.9 5.5 51104
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 2.157 2.164 98.5 0.661 0.79 5.8
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 FREE R-VALUE 5N0O 2.16 78.06 48538 2499 99.79 0.20142 0.20007 0.2052 0.22628 0.2293 RANDOM 72.243
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] 0.12 -0.66 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.593 r_dihedral_angle_4_deg 17.933 r_dihedral_angle_3_deg 12.266 r_dihedral_angle_1_deg 5.659 r_long_range_B_other 4.555 r_long_range_B_refined 4.55 r_mcangle_it 2.321 r_mcangle_other 2.321 r_scangle_other 2.176 r_mcbond_it 1.33
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.593 r_dihedral_angle_4_deg 17.933 r_dihedral_angle_3_deg 12.266 r_dihedral_angle_1_deg 5.659 r_long_range_B_other 4.555 r_long_range_B_refined 4.55 r_mcangle_it 2.321 r_mcangle_other 2.321 r_scangle_other 2.176 r_mcbond_it 1.33 r_mcbond_other 1.33 r_angle_refined_deg 1.315 r_scbond_it 1.279 r_scbond_other 1.278 r_angle_other_deg 0.933 r_chiral_restr 0.076 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 5728 Nucleic Acid Atoms Solvent Atoms 120 Heterogen Atoms 60
Software Software Software Name Purpose REFMAC refinement xia2 data reduction xia2 data scaling PHASER phasing