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DtpB in complex with photocaged nitric oxide, 1.24 s, 0.81 microjoule, SSX
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 6-10 mg/ml of protein in 50 mm sodium acetate, 150 mm NaCl pH 5 mixed with 150 mM MgCl2, 150 mm HEPES, 20 % PEG 4000, pH 7.5.
Crystal Properties Matthews coefficient Solvent content 2.45 49.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.124 α = 90 b = 122.929 β = 90 c = 195.552 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 PIXEL DECTRIS PILATUS3 6M 2023-02-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 1.000 Diamond I24
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 Oxford silicon chip fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 Geobrick and Smaract
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 undefined (fs) undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1
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 2.4 79.71 100 0.971 0.192 5.1 28.7 82839
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 2.4 2.44 0.343 0.878
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 (All) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.4 79.71 82839 4185 99.994 0.18 0.1778 0.2262 0.1803 37.789
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] 0.044 0.101 -0.146
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.955 r_dihedral_angle_6_deg 11.061 r_dihedral_angle_1_deg 5.809 r_lrange_it 4.736 r_dihedral_angle_2_deg 3.44 r_scangle_it 2.803 r_mcangle_it 2.418 r_scbond_it 1.616 r_mcbond_it 1.344 r_angle_refined_deg 1.015
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 12.955 r_dihedral_angle_6_deg 11.061 r_dihedral_angle_1_deg 5.809 r_lrange_it 4.736 r_dihedral_angle_2_deg 3.44 r_scangle_it 2.803 r_mcangle_it 2.418 r_scbond_it 1.616 r_mcbond_it 1.344 r_angle_refined_deg 1.015 r_nbtor_refined 0.295 r_nbd_refined 0.174 r_symmetry_nbd_refined 0.164 r_symmetry_xyhbond_nbd_refined 0.15 r_xyhbond_nbd_refined 0.108 r_chiral_restr 0.077 r_bond_refined_d 0.002 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13975 Nucleic Acid Atoms Solvent Atoms 523 Heterogen Atoms 270
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data reduction xia2 data scaling MOLREP phasing Coot model building