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Crystal structure of MTAP from Aeropyrum pernix complex with MTA at 323K, 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 2.27398872 45.84
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.851 α = 90 b = 78.851 β = 90 c = 233.656 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 323 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 1.59 44.39 100 0.053 0.059 0.026 1 28.3 10 38079
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) 1.59 1.62 100 1.024 1.14 0.498 0.674 2.4 10.2
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 1.59 44.39 38078 1923 99.963 0.138 0.1372 0.1506 0.1619 0.1702 28.357
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] 0.239 0.12 0.239 -0.776
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.854 r_dihedral_angle_3_deg 13.711 r_lrange_other 10.482 r_lrange_it 10.481 r_scangle_it 8.488 r_scangle_other 8.485 r_dihedral_angle_2_deg 7.014 r_dihedral_angle_1_deg 6.983 r_scbond_it 5.464 r_scbond_other 5.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.854 r_dihedral_angle_3_deg 13.711 r_lrange_other 10.482 r_lrange_it 10.481 r_scangle_it 8.488 r_scangle_other 8.485 r_dihedral_angle_2_deg 7.014 r_dihedral_angle_1_deg 6.983 r_scbond_it 5.464 r_scbond_other 5.464 r_mcangle_it 3.779 r_mcangle_other 3.778 r_mcbond_it 2.605 r_mcbond_other 2.604 r_angle_refined_deg 1.96 r_angle_other_deg 0.646 r_nbd_refined 0.223 r_symmetry_nbd_other 0.203 r_nbd_other 0.193 r_nbtor_refined 0.183 r_xyhbond_nbd_refined 0.114 r_symmetry_nbd_refined 0.113 r_chiral_restr 0.095 r_symmetry_nbtor_other 0.088 r_symmetry_xyhbond_nbd_refined 0.083 r_dihedral_angle_other_2_deg 0.066 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 56 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction