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The structure of the YcfA-GTP from Erwinia amylovora
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details in silico model AlphaFold
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 289.15 0.2 M sodium malonate pH 7.0 and 20% PEG3350
Crystal Properties Matthews coefficient Solvent content 2.9 57.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 68.174 α = 90 b = 134.366 β = 98.35 c = 233.837 γ = 90
Symmetry Space Group P 1 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 PILATUS 6M 2022-08-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL18U1 0.979 SSRF BL18U1
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 2.59 47.51 99.75 0.993 9.06 6.8 128775
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 2.594 2.661 0.608
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 (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 2.59 47.51 122219 6531 99.79 0.21331 0.21096 0.2183 0.25746 0.2587 RANDOM 52.65
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] 0.97 0.24 -1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.468 r_dihedral_angle_2_deg 12.884 r_long_range_B_refined 10.328 r_long_range_B_other 10.326 r_scangle_other 8.811 r_mcangle_other 7.277 r_mcangle_it 7.276 r_dihedral_angle_1_deg 6.424 r_scbond_it 6.339 r_scbond_other 6.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_3_deg 16.468 r_dihedral_angle_2_deg 12.884 r_long_range_B_refined 10.328 r_long_range_B_other 10.326 r_scangle_other 8.811 r_mcangle_other 7.277 r_mcangle_it 7.276 r_dihedral_angle_1_deg 6.424 r_scbond_it 6.339 r_scbond_other 6.338 r_mcbond_it 5.264 r_mcbond_other 5.264 r_angle_refined_deg 2.383 r_angle_other_deg 0.784 r_chiral_restr 0.12 r_bond_refined_d 0.014 r_gen_planes_refined 0.01 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_dihedral_angle_4_deg r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 24108 Nucleic Acid Atoms Solvent Atoms 664 Heterogen Atoms 224
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing