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mosquitocidal Cry11Ba determined at pH 6.5 from naturally-occurring nanocrystals by Serial femtosecond crystallography
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7QX4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 IN CELL 6.5 303 crystallized in vivo
Crystal Properties Matthews coefficient Solvent content 2.35 47.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 168.245 α = 90 b = 158.528 β = 90 c = 57.534 γ = 90
Symmetry Space Group P 21 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 298 PIXEL CS-PAD CXI-2 2016-09-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 FREE ELECTRON LASER SLAC LCLS BEAMLINE CXI 1.304373 SLAC LCLS CXI
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 microfluidic electrokinetic sample holder injection
Measurement Diffraction ID Pulse Duration Pulse Repetition Rate Focal Spot Size Pulse Energy Photons Per Pulse 1 50 (fs) 120 1 undefined (KeV)
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1
Injection Diffraction ID Description Flow Rate Injector Diameter Injection Power Injector Nozzle Filter Size Carrier Solvent 1 microfluidic electrokinetic sample holder undefined (µl/min) undefined (µm)
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 42.1 100 0.991 0.0145 4.7 57.9 61141
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 2.44 100 0.359 0.849 17.1
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 7QX4 2.4 42.1 55060 5991 99.92 0.187 0.1826 0.1903 0.2309 0.2344 47.7
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] -1.446 -0.253 1.699
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.531 r_dihedral_angle_3_deg 12.513 r_dihedral_angle_4_deg 11.891 r_lrange_it 7.983 r_lrange_other 7.964 r_scangle_it 6.411 r_scangle_other 6.411 r_dihedral_angle_1_deg 6.112 r_mcangle_it 5.216 r_mcangle_other 5.216
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.531 r_dihedral_angle_3_deg 12.513 r_dihedral_angle_4_deg 11.891 r_lrange_it 7.983 r_lrange_other 7.964 r_scangle_it 6.411 r_scangle_other 6.411 r_dihedral_angle_1_deg 6.112 r_mcangle_it 5.216 r_mcangle_other 5.216 r_scbond_it 4.253 r_scbond_other 4.253 r_mcbond_it 3.494 r_mcbond_other 3.487 r_angle_other_deg 2.266 r_angle_refined_deg 1.324 r_nbd_other 0.223 r_symmetry_nbd_other 0.211 r_nbd_refined 0.179 r_nbtor_refined 0.168 r_symmetry_nbd_refined 0.159 r_xyhbond_nbd_refined 0.156 r_symmetry_xyhbond_nbd_refined 0.143 r_symmetry_xyhbond_nbd_other 0.085 r_symmetry_nbtor_other 0.068 r_chiral_restr 0.054 r_bond_other_d 0.035 r_bond_refined_d 0.008 r_gen_planes_other 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10064 Nucleic Acid Atoms Solvent Atoms 622 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement cctbx.xfel data reduction PHASER phasing cctbx.xfel data scaling