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The structure of xanthosine methyltransferase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EFJ PDB ENTRY 2EFJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 25% PEG 3350, 200mM Li2SO4, 100mM Tris-HCl, 1mM SAH, 1mM xanthosine, 2mM DTT, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.34 47.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.59 α = 90 b = 119.8 β = 102.16 c = 116.4 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 4 2005-11-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.9393 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.2 30 95.2 0.079 13.1 75624 74901
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.2 2.3 93.4 0.443 3 10071
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 (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2EFJ 2.2 30 71794 3830 96.68 0.233 0.23 0.284 0.2573 RANDOM 44.845
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] -0.83 0.42 -1.88 2.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.845 r_dihedral_angle_3_deg 19.096 r_dihedral_angle_4_deg 12.874 r_dihedral_angle_1_deg 6.826 r_scangle_it 3.162 r_scbond_it 2.093 r_angle_refined_deg 1.734 r_mcangle_it 1.519 r_mcbond_it 0.897 r_symmetry_vdw_refined 0.316
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.845 r_dihedral_angle_3_deg 19.096 r_dihedral_angle_4_deg 12.874 r_dihedral_angle_1_deg 6.826 r_scangle_it 3.162 r_scbond_it 2.093 r_angle_refined_deg 1.734 r_mcangle_it 1.519 r_mcbond_it 0.897 r_symmetry_vdw_refined 0.316 r_nbtor_refined 0.313 r_symmetry_hbond_refined 0.286 r_nbd_refined 0.233 r_xyhbond_nbd_refined 0.197 r_chiral_restr 0.114 r_bond_refined_d 0.015 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10668 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms 184
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction XSCALE data scaling PHASER phasing