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AtoB in complex with substrate analogue
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6U9I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 291.15 2 M ammonium sulfate, 0.2 M potassium sodium tartrate tetrahydrate, and 0.1 M sodium citrate (pH 5.6)
Crystal Properties Matthews coefficient Solvent content 2.66 53.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.265 α = 90 b = 92.917 β = 90.184 c = 44.265 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293.15 PIXEL DECTRIS EIGER2 X 9M 2023-10-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL02U1 0.97915 SSRF BL02U1
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 1.6 29.71 99.24 0.998 14.16 5.6 42230
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 1.65 1.709 0.815
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 NONE 6U9I 1.65 29.71 42230 1998 98.271 0.127 0.1258 0.137 0.1584 0.1665 24.929
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] -3.066 1.598 17.917 -14.851
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.929 r_dihedral_angle_3_deg 16.284 r_dihedral_angle_2_deg 8.173 r_dihedral_angle_1_deg 6.894 r_lrange_it 5.263 r_rigid_bond_restr 5.05 r_lrange_other 4.862 r_scangle_it 3.775 r_scangle_other 3.774 r_mcangle_it 3.375
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.929 r_dihedral_angle_3_deg 16.284 r_dihedral_angle_2_deg 8.173 r_dihedral_angle_1_deg 6.894 r_lrange_it 5.263 r_rigid_bond_restr 5.05 r_lrange_other 4.862 r_scangle_it 3.775 r_scangle_other 3.774 r_mcangle_it 3.375 r_mcangle_other 3.374 r_scbond_other 2.84 r_scbond_it 2.838 r_mcbond_it 2.471 r_mcbond_other 2.471 r_angle_refined_deg 1.798 r_angle_other_deg 0.596 r_nbd_other 0.29 r_symmetry_nbd_refined 0.238 r_xyhbond_nbd_refined 0.235 r_symmetry_xyhbond_nbd_refined 0.233 r_nbd_refined 0.227 r_symmetry_nbd_other 0.201 r_nbtor_refined 0.18 r_symmetry_nbtor_other 0.089 r_chiral_restr 0.087 r_bond_refined_d 0.012 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2336 Nucleic Acid Atoms Solvent Atoms 220 Heterogen Atoms 82
Software Software Software Name Purpose PHENIX refinement HKL-3000 data reduction HKL-3000 data scaling PHASER phasing