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DtpB in complex with photocaged nitric oxide, 1.24 s, 64.4 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 49.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.184 α = 90 b = 123.175 β = 90 c = 195.465 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 fixed target
Fixed Target Diffraction ID Description Sample Holding Support Base Motion control Details Sample Solvent 1 Oxford silicon chip 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 79.75 100 0.976 0.214 6.4 39.3 83011
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 0.346 1.332
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 6yrj 2.4 79.75 83011 4198 99.995 0.189 0.188 0.1881 0.2138 0.2139 42.614
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] -0.354 0.293 0.061
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.929 r_dihedral_angle_6_deg 13.171 r_lrange_it 6.572 r_dihedral_angle_1_deg 6.167 r_dihedral_angle_2_deg 5.674 r_scangle_it 4.759 r_mcangle_it 3.345 r_scbond_it 2.877 r_mcbond_it 1.941 r_angle_refined_deg 1.217
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.929 r_dihedral_angle_6_deg 13.171 r_lrange_it 6.572 r_dihedral_angle_1_deg 6.167 r_dihedral_angle_2_deg 5.674 r_scangle_it 4.759 r_mcangle_it 3.345 r_scbond_it 2.877 r_mcbond_it 1.941 r_angle_refined_deg 1.217 r_nbtor_refined 0.297 r_symmetry_nbd_refined 0.231 r_symmetry_xyhbond_nbd_refined 0.227 r_nbd_refined 0.187 r_xyhbond_nbd_refined 0.106 r_chiral_restr 0.095 r_ncsr_local_group_5 0.086 r_ncsr_local_group_11 0.086 r_ncsr_local_group_15 0.085 r_ncsr_local_group_13 0.081 r_ncsr_local_group_8 0.08 r_ncsr_local_group_14 0.08 r_ncsr_local_group_4 0.078 r_ncsr_local_group_2 0.077 r_ncsr_local_group_9 0.077 r_ncsr_local_group_12 0.077 r_ncsr_local_group_10 0.076 r_ncsr_local_group_6 0.072 r_ncsr_local_group_1 0.07 r_ncsr_local_group_3 0.07 r_ncsr_local_group_7 0.07 r_gen_planes_refined 0.004 r_bond_refined_d 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13966 Nucleic Acid Atoms Solvent Atoms 420 Heterogen Atoms 270
Software Software Software Name Purpose REFMAC refinement DIALS data reduction xia2 data reduction xia2 data scaling MOLREP phasing Coot model building