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Crystal structure of MTAP from Aeropyrum pernix complex with MTA at 293K, 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 intou 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 citarate pH5.4, 5mM MTA. Crystals soaked in 0.1M potassium phosphate pH7.0 with 5mM MTA.
Crystal Properties Matthews coefficient Solvent content 2.26955032 45.8379135
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.788 α = 90 b = 78.788 β = 90 c = 233.573 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 293 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 1.64 44.36 100 0.069 0.077 0.033 1 25 10 34662
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) 1.64 1.67 100 0.976 1.089 0.475 0.675 2.8 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 1.64 44.36 34660 1685 99.968 0.141 0.1397 0.152 0.1592 0.168 25.255
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] 0.195 0.098 0.195 -0.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.283 r_dihedral_angle_3_deg 13.669 r_lrange_it 8.826 r_lrange_other 8.823 r_dihedral_angle_2_deg 8.528 r_scangle_it 7.198 r_scangle_other 7.196 r_dihedral_angle_1_deg 7.001 r_scbond_it 4.641 r_scbond_other 4.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_6_deg 16.283 r_dihedral_angle_3_deg 13.669 r_lrange_it 8.826 r_lrange_other 8.823 r_dihedral_angle_2_deg 8.528 r_scangle_it 7.198 r_scangle_other 7.196 r_dihedral_angle_1_deg 7.001 r_scbond_it 4.641 r_scbond_other 4.64 r_mcangle_it 3.173 r_mcangle_other 3.172 r_mcbond_it 2.231 r_mcbond_other 2.231 r_angle_refined_deg 1.923 r_angle_other_deg 0.642 r_nbd_refined 0.214 r_symmetry_nbd_other 0.198 r_nbtor_refined 0.181 r_nbd_other 0.176 r_xyhbond_nbd_refined 0.13 r_chiral_restr 0.096 r_symmetry_xyhbond_nbd_refined 0.089 r_symmetry_nbtor_other 0.086 r_symmetry_nbd_refined 0.074 r_dihedral_angle_other_2_deg 0.044 r_gen_planes_refined 0.011 r_bond_refined_d 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 70 Heterogen Atoms 25
Software Software Software Name Purpose REFMAC refinement Coot model building MOLREP phasing Aimless data scaling XDS data reduction