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Crystal structure of Escherichia coli CyaY by fixed target serial synchrotron crystallography
Serial Crystallography (SX)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1EW4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 277 4 M NaCl, 0.1 M citric acid, pH:4
Crystal Properties Matthews coefficient Solvent content 2.44 49.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.2 α = 90 b = 45.2 β = 90 c = 101.1 γ = 120
Symmetry Space Group P 32 2 1
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 EIGER2 R 4M 2024-05-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2) 0.976 PETRA III, EMBL c/o DESY P14 (MX2)
Serial Crystallography Sample delivery method Diffraction ID Description Sample Delivery Method 1 fixed target
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 1.7 39.14 98.87 0.36 1.99 10.5 13634
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 1.7 1.83 0.06
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 1EW4 1.7 39.14 13633 649 98.984 0.262 0.2596 0.2602 0.3129 0.3137 14.032
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] -0.141 -0.07 -0.141 0.456
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.61 r_dihedral_angle_6_deg 16.348 r_dihedral_angle_2_deg 13.656 r_dihedral_angle_1_deg 6.989 r_lrange_it 4.892 r_lrange_other 4.888 r_scangle_it 2.699 r_scangle_other 2.697 r_mcangle_it 2.627 r_mcangle_other 2.625
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 17.61 r_dihedral_angle_6_deg 16.348 r_dihedral_angle_2_deg 13.656 r_dihedral_angle_1_deg 6.989 r_lrange_it 4.892 r_lrange_other 4.888 r_scangle_it 2.699 r_scangle_other 2.697 r_mcangle_it 2.627 r_mcangle_other 2.625 r_angle_refined_deg 2.276 r_mcbond_it 1.672 r_mcbond_other 1.664 r_scbond_it 1.649 r_scbond_other 1.647 r_angle_other_deg 0.913 r_xyhbond_nbd_refined 0.3 r_symmetry_xyhbond_nbd_refined 0.263 r_nbd_refined 0.198 r_symmetry_nbd_other 0.177 r_nbtor_refined 0.175 r_nbd_other 0.164 r_symmetry_nbd_refined 0.15 r_chiral_restr 0.112 r_symmetry_nbtor_other 0.078 r_symmetry_xyhbond_nbd_other 0.044 r_bond_refined_d 0.013 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 863 Nucleic Acid Atoms Solvent Atoms 43 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling REFMAC phasing