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DtpB in complex with photocaged nitric oxide, 100 microsecond, 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 293 50 mM HEPES pH 7.5, 150 mM Magnesium chloride 20% PEG4000
Crystal Properties Matthews coefficient Solvent content 2.64 53.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.475 α = 90 b = 124.392 β = 90 c = 193.508 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 293 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 1.52 104.64 100 0.996 19.4 167 322685
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 1.52 1.55 100 0.317
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 1.52 45.13 320258 2084 99.89 0.20916 0.20899 0.2198 0.2353 0.245 RANDOM 22.938
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] -0.15 0.14 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.397 r_dihedral_angle_2_deg 8.084 r_long_range_B_refined 7.599 r_long_range_B_other 7.561 r_dihedral_angle_1_deg 7.215 r_scangle_other 5.902 r_scbond_it 3.845 r_scbond_other 3.832 r_mcangle_it 3.499 r_mcangle_other 3.499
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.397 r_dihedral_angle_2_deg 8.084 r_long_range_B_refined 7.599 r_long_range_B_other 7.561 r_dihedral_angle_1_deg 7.215 r_scangle_other 5.902 r_scbond_it 3.845 r_scbond_other 3.832 r_mcangle_it 3.499 r_mcangle_other 3.499 r_mcbond_it 2.351 r_mcbond_other 2.351 r_angle_refined_deg 1.954 r_angle_other_deg 0.683 r_chiral_restr 0.092 r_bond_refined_d 0.011 r_gen_planes_refined 0.01 r_gen_planes_other 0.006 r_bond_other_d 0.002 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13944 Nucleic Acid Atoms Solvent Atoms 1078 Heterogen Atoms 278
Software Software Software Name Purpose REFMAC refinement xia2 data scaling xia2 data reduction PHASER phasing