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SSX structure of Arabidopsis thaliana Pdx1.3 grown in seeded batch conditions
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 BATCH MODE 7 294 600 mM Sodium citrate and 100 mM HEPES pH 7
Crystal Properties Matthews coefficient Solvent content 2.86 57.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 177.9 α = 90 b = 177.9 β = 90 c = 117.3 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 19325 20268 19325
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 93.33 100 0.96 4.4 47.4 47878 49.36
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 0.17 0.5 45.18
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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.5 64.472 47873 2316 99.994 0.169 0.1676 0.1934 0.1769 RANDOM 59.434
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] -0.005 -0.002 -0.005 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.18 r_dihedral_angle_6_deg 14.129 r_lrange_other 11.013 r_lrange_it 11.006 r_scangle_it 9.179 r_scangle_other 9.099 r_dihedral_angle_2_deg 7.892 r_mcangle_it 6.57 r_mcangle_other 6.57 r_dihedral_angle_1_deg 6.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 15.18 r_dihedral_angle_6_deg 14.129 r_lrange_other 11.013 r_lrange_it 11.006 r_scangle_it 9.179 r_scangle_other 9.099 r_dihedral_angle_2_deg 7.892 r_mcangle_it 6.57 r_mcangle_other 6.57 r_dihedral_angle_1_deg 6.304 r_scbond_it 5.847 r_scbond_other 5.714 r_mcbond_it 4.34 r_mcbond_other 4.339 r_angle_refined_deg 1.407 r_angle_other_deg 0.458 r_nbd_refined 0.213 r_symmetry_nbd_other 0.199 r_nbtor_refined 0.173 r_symmetry_nbd_refined 0.157 r_nbd_other 0.152 r_symmetry_xyhbond_nbd_refined 0.141 r_xyhbond_nbd_refined 0.135 r_symmetry_nbtor_other 0.082 r_ncsr_local_group_5 0.07 r_ncsr_local_group_6 0.07 r_ncsr_local_group_3 0.064 r_chiral_restr 0.062 r_ncsr_local_group_1 0.062 r_ncsr_local_group_2 0.061 r_ncsr_local_group_4 0.059 r_bond_refined_d 0.005 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8056 Nucleic Acid Atoms Solvent Atoms 181 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement CrystFEL data reduction CrystFEL data scaling MOLREP phasing