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DtpB in complex with photocaged nitric oxide, 10 ms, 30 microjoule, SFX
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6YRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 291 50 mM HEPES pH 7.5, 150 mM Magnesium chloride, 20% (w/v) PEG4000
Crystal Properties Matthews coefficient Solvent content 2.63 53.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.168 α = 90 b = 123.062 β = 90 c = 195.276 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 291 CCD RAYONIX MX300-HS 2023-11-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SACLA BEAMLINE BL2 1.127 SACLA BL2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.69 104.11 100 0.988 15.04 95 234283
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.69 1.72 100 0.314 1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 1.69 104.11 234283 994 100 0.18692 0.19 0.1842 0.218 0.1878 RANDOM 25.58
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] 0.02 -0.18 0.15
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 16.981 r_long_range_B_other 16.718 r_scangle_other 13.753 r_dihedral_angle_3_deg 13.463 r_mcangle_it 9.755 r_mcangle_other 9.755 r_scbond_it 9.614 r_scbond_other 9.61 r_dihedral_angle_2_deg 8.518 r_mcbond_it 6.816
RMS Deviations Key Refinement Restraint Deviation r_long_range_B_refined 16.981 r_long_range_B_other 16.718 r_scangle_other 13.753 r_dihedral_angle_3_deg 13.463 r_mcangle_it 9.755 r_mcangle_other 9.755 r_scbond_it 9.614 r_scbond_other 9.61 r_dihedral_angle_2_deg 8.518 r_mcbond_it 6.816 r_mcbond_other 6.79 r_dihedral_angle_1_deg 6.559 r_rigid_bond_restr 4.737 r_angle_refined_deg 2.004 r_angle_other_deg 0.698 r_chiral_restr 0.094 r_bond_refined_d 0.012 r_gen_planes_refined 0.009 r_gen_planes_other 0.006 r_bond_other_d 0.001 r_dihedral_angle_4_deg 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_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13975 Nucleic Acid Atoms Solvent Atoms 972 Heterogen Atoms 270
Software Software Software Name Purpose REFMAC refinement DIALS data scaling DIALS data reduction PHASER phasing