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Crystal structure of MTAP from Aeropyrum pernix complex with MTA at 343K, 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#200,0.1 M
phosphate citrate pH 5.4, 5 mM MTA. Crystals soaked in 0.1M potassium phosphate pH7.0 with 5mM MTA.
Crystal Properties Matthews coefficient Solvent content 2.28745079 46.2617569
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.021 α = 90 b = 79.021 β = 90 c = 234.029 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 343 PIXEL DECTRIS EIGER X 16M 2025-03-09 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 1.72 44.47 100 0.098 0.108 0.047 1 23.7 10 30381
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) 1.72 1.75 100 1.2 1.343 0.596 0.675 2.3 9.7
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 1.72 44.47 30379 1473 99.961 0.139 0.1373 0.1494 0.1683 0.1782 29.637
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] 0.293 0.147 0.293 -0.952
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.452 r_dihedral_angle_3_deg 14.512 r_dihedral_angle_2_deg 10.699 r_lrange_it 10.514 r_lrange_other 10.514 r_scangle_it 8.408 r_scangle_other 8.406 r_dihedral_angle_1_deg 7.301 r_scbond_it 5.303 r_scbond_other 5.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 15.452 r_dihedral_angle_3_deg 14.512 r_dihedral_angle_2_deg 10.699 r_lrange_it 10.514 r_lrange_other 10.514 r_scangle_it 8.408 r_scangle_other 8.406 r_dihedral_angle_1_deg 7.301 r_scbond_it 5.303 r_scbond_other 5.303 r_mcangle_it 4.183 r_mcangle_other 4.181 r_mcbond_it 2.852 r_mcbond_other 2.85 r_angle_refined_deg 1.926 r_angle_other_deg 0.628 r_nbd_refined 0.216 r_symmetry_nbd_other 0.196 r_nbd_other 0.189 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.146 r_symmetry_xyhbond_nbd_refined 0.102 r_chiral_restr 0.093 r_symmetry_nbtor_other 0.088 r_symmetry_nbd_refined 0.068 r_dihedral_angle_other_2_deg 0.039 r_bond_refined_d 0.01 r_gen_planes_refined 0.01 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