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DtpB in complex with photocaged nitric oxide, 10 ms, 10 microjoule, SFX
Serial Crystallography (SX)
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 53.16
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.073 α = 90 b = 122.875 β = 90 c = 194.936 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 300 CCD RAYONIX MX-300 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
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 10 (fs) 30000 10.993 (KeV)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) R Split (All) 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 1.56 103.95 100 0.994 0.096 18.1 168.6 295889
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) R Split (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.59 0.316 1.256 0.9
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 1.56 44.68 293539 2027 99.89 0.20891 0.20874 0.2195 0.23363 0.2437 RANDOM 23.355
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] -0.29 0.14 0.15
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.268 r_dihedral_angle_2_deg 8.51 r_long_range_B_refined 7.509 r_long_range_B_other 7.468 r_dihedral_angle_1_deg 6.431 r_scangle_other 5.945 r_scbond_it 3.848 r_scbond_other 3.837 r_mcangle_it 3.545 r_mcangle_other 3.545
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.268 r_dihedral_angle_2_deg 8.51 r_long_range_B_refined 7.509 r_long_range_B_other 7.468 r_dihedral_angle_1_deg 6.431 r_scangle_other 5.945 r_scbond_it 3.848 r_scbond_other 3.837 r_mcangle_it 3.545 r_mcangle_other 3.545 r_mcbond_it 2.418 r_mcbond_other 2.417 r_angle_refined_deg 1.98 r_angle_other_deg 0.703 r_chiral_restr 0.104 r_bond_refined_d 0.012 r_gen_planes_refined 0.01 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_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 1102 Heterogen Atoms 270
Software Software Software Name Purpose REFMAC refinement DIALS data scaling DIALS data reduction PHASER phasing