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Cryogenic temprature crystal structure of Escherichia coli CyaY
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 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.486 α = 90 b = 44.486 β = 90 c = 98.165 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 100 PIXEL DECTRIS EIGER2 XE 16M 2024-11-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 0.95373 Diamond I04
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 1.06 98.17 98.5 0.99 13.5 10.2 51068
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 1.06 1.08 0.35
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 1.06 38.526 51068 1882 98.442 0.219 0.2178 0.2191 0.2476 0.2484 15.903
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] -0.192 -0.096 -0.192 0.624
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.621 r_dihedral_angle_6_deg 15.611 r_dihedral_angle_3_deg 13.267 r_lrange_it 5.728 r_dihedral_angle_1_deg 5.363 r_scangle_it 4.272 r_scbond_it 2.838 r_angle_refined_deg 2.301 r_mcangle_it 1.467 r_mcbond_it 1.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 17.621 r_dihedral_angle_6_deg 15.611 r_dihedral_angle_3_deg 13.267 r_lrange_it 5.728 r_dihedral_angle_1_deg 5.363 r_scangle_it 4.272 r_scbond_it 2.838 r_angle_refined_deg 2.301 r_mcangle_it 1.467 r_mcbond_it 1.016 r_symmetry_nbd_refined 0.389 r_nbtor_refined 0.315 r_xyhbond_nbd_refined 0.255 r_nbd_refined 0.228 r_symmetry_xyhbond_nbd_refined 0.193 r_chiral_restr 0.176 r_gen_planes_refined 0.013 r_bond_refined_d 0.012
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 863 Nucleic Acid Atoms Solvent Atoms 124 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling REFMAC phasing