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SSX structure of Arabidopsis thaliana Pdx1.3 grown in microfluidic droplets
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7NHF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROFLUIDIC 7 294 600 mM Sodium citrate and 100 mM HEPES pH 7
Crystal Properties Matthews coefficient Solvent content 2.99 58.86
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 180.3 α = 90 b = 180.3 β = 90 c = 119.2 γ = 120
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 PSI JUNGFRAU 4M 2023-01-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.07 ESRF ID29
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 SOS Chip fixed target
Data Reduction Diffraction ID Frames Indexed Crystal Hits Frames Indexed Latices Merged 1 20635 20827 20635
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 2.5 94.75 100 0.96 5 44.2 50011 45.27
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 2.5 2.54 100 0.27 0.8 44.2
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-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.5 65.396 50003 2510 99.984 0.16 0.1584 0.1671 0.1883 0.1929 59.187
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] 0.006 0.003 0.006 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.633 r_dihedral_angle_6_deg 14.104 r_lrange_it 11.962 r_lrange_other 11.951 r_scangle_it 9.728 r_scangle_other 9.702 r_dihedral_angle_2_deg 9.081 r_mcangle_it 7.523 r_mcangle_other 7.523 r_dihedral_angle_1_deg 6.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 14.633 r_dihedral_angle_6_deg 14.104 r_lrange_it 11.962 r_lrange_other 11.951 r_scangle_it 9.728 r_scangle_other 9.702 r_dihedral_angle_2_deg 9.081 r_mcangle_it 7.523 r_mcangle_other 7.523 r_dihedral_angle_1_deg 6.5 r_scbond_it 6.193 r_scbond_other 6.109 r_mcbond_it 4.956 r_mcbond_other 4.956 r_angle_refined_deg 1.511 r_angle_other_deg 0.504 r_nbd_refined 0.206 r_symmetry_nbd_other 0.195 r_nbtor_refined 0.168 r_nbd_other 0.162 r_symmetry_nbd_refined 0.14 r_xyhbond_nbd_refined 0.135 r_symmetry_xyhbond_nbd_refined 0.107 r_symmetry_nbtor_other 0.079 r_ncsr_local_group_3 0.078 r_ncsr_local_group_6 0.075 r_chiral_restr 0.072 r_ncsr_local_group_5 0.07 r_ncsr_local_group_2 0.063 r_ncsr_local_group_1 0.06 r_ncsr_local_group_4 0.059 r_bond_refined_d 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8088 Nucleic Acid Atoms Solvent Atoms 186 Heterogen Atoms 72
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling MOLREP phasing