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Crystal structure of MTAP from Aeropyrum pernix complex with MTA at 333K, Soaked in potassium phosphate pH7.0 with MTA
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WTA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 COUNTER-DIFFUSION 5.4 293.2 The mixture of protein solution and agarose was filled into a glass capillary, and the capillary was immersed in the reservoir solution for crystallization. The composition of the reservoir solution was as follows 15%(v/v)PEG#200, 0.1M phosphate citrate pH5.4, 5mM MTA. Crystals soaked in 0.1M potassium phosphate pH7.0 with 5mM MTA.
Crystal Properties Matthews coefficient Solvent content 2.27689242 46.0125628
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.875 α = 90 b = 78.875 β = 90 c = 233.812 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 333 PIXEL DECTRIS EIGER X 16M 2024-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-17A 0.98 Photon Factory BL-17A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.67 44.41 100 0.059 0.066 0.029 1 25.2 10 32977
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.67 1.7 100 1.008 1.123 0.493 0.691 2.4 10
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 1WTA 1.67 44.41 32975 1606 99.97 0.138 0.1368 0.1488 0.1644 0.1705 29.617
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] 0.268 0.134 0.268 -0.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.55 r_dihedral_angle_3_deg 13.861 r_lrange_other 10.001 r_lrange_it 9.997 r_scangle_it 8.364 r_scangle_other 8.362 r_dihedral_angle_2_deg 8.137 r_dihedral_angle_1_deg 6.91 r_scbond_it 5.321 r_scbond_other 5.321
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.55 r_dihedral_angle_3_deg 13.861 r_lrange_other 10.001 r_lrange_it 9.997 r_scangle_it 8.364 r_scangle_other 8.362 r_dihedral_angle_2_deg 8.137 r_dihedral_angle_1_deg 6.91 r_scbond_it 5.321 r_scbond_other 5.321 r_mcangle_it 4.071 r_mcangle_other 4.07 r_mcbond_it 2.893 r_mcbond_other 2.889 r_angle_refined_deg 1.946 r_angle_other_deg 0.643 r_nbd_refined 0.219 r_symmetry_nbd_other 0.2 r_nbd_other 0.185 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.122 r_symmetry_xyhbond_nbd_refined 0.116 r_symmetry_nbd_refined 0.097 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.086 r_dihedral_angle_other_2_deg 0.022 r_bond_refined_d 0.011 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 2142 Nucleic Acid Atoms Solvent Atoms 52 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction