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Crystal structure of MTAP from Aeropyrum pernix complex with MTA at 100K, 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 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 2.17883253 43.58209
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 77.66 α = 90 b = 77.66 β = 90 c = 230.798 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 100 PIXEL DECTRIS EIGER X 16M 2024-12-09 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 1.19 43.79 100 0.053 0.06 0.026 1 21.1 9.7 86141
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) 1.19 1.21 100 0.597 0.666 0.294 0.665 3.1 9.9
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 1.19 43.79 86126 4322 99.967 0.131 0.1299 0.132 0.1572 0.1564 16.29
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] 0.143 0.071 0.143 -0.464
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.885 r_lrange_it 12.54 r_lrange_other 12.481 r_dihedral_angle_3_deg 12.162 r_dihedral_angle_2_deg 10.308 r_scangle_it 10.014 r_scangle_other 10.011 r_scbond_it 7.227 r_scbond_other 7.224 r_dihedral_angle_1_deg 6.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.885 r_lrange_it 12.54 r_lrange_other 12.481 r_dihedral_angle_3_deg 12.162 r_dihedral_angle_2_deg 10.308 r_scangle_it 10.014 r_scangle_other 10.011 r_scbond_it 7.227 r_scbond_other 7.224 r_dihedral_angle_1_deg 6.91 r_mcangle_it 6.521 r_mcangle_other 6.519 r_mcbond_it 4.565 r_mcbond_other 4.56 r_rigid_bond_restr 4.289 r_angle_refined_deg 1.904 r_angle_other_deg 0.689 r_nbd_refined 0.219 r_symmetry_nbd_other 0.195 r_nbd_other 0.191 r_nbtor_refined 0.181 r_xyhbond_nbd_refined 0.129 r_dihedral_angle_other_2_deg 0.123 r_symmetry_nbd_refined 0.115 r_chiral_restr 0.109 r_symmetry_nbtor_other 0.083 r_symmetry_xyhbond_nbd_refined 0.083 r_gen_planes_refined 0.013 r_bond_refined_d 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 133 Heterogen Atoms 59
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction