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Crystal structure of Thiopurine methyltransferase (18204406) from Mus musculus at 1.35 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BZG pdb entry 2bzg
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP, NANODROP 5.6 293 5.0% Glycerol, 19.0% iso-Propanol, 19.0% PEG-4000, 0.1M Citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.43 48.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.988 α = 90 b = 70.554 β = 115.7 c = 72.593 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 MARMOSAIC 325 mm CCD 2005-07-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 1.25 50 79.4 0.033 15.4 2.7 125498
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) 1.25 1.29 46.9 0.325 1.5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R pdb entry 2bzg 1.25 35.9 125430 4154 79.4 0.139 0.136 0.1324 0.193 0.1876 RANDOM EXPANDED BY TWIN LAW 18.394
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] -1.26 -0.44 1.96 -1.07
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 11 3551 4169
RMS Deviations Key Refinement Restraint Deviation s_from_restr_planes 0.389 s_approx_iso_adps 0.105 s_similar_dist 0.067 s_zero_chiral_vol 0.065 s_non_zero_chiral_vol 0.063 s_similar_adp_cmpnt 0.04 s_angle_d 0.032 s_anti_bump_dis_restr 0.023 s_bond_d 0.012 s_rigid_bond_adp_cmpnt 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3796 Nucleic Acid Atoms Solvent Atoms 402 Heterogen Atoms 52
Software Software Software Name Purpose SHELXL-97 refinement SCALEPACK data scaling PDB_EXTRACT data extraction DENZO data reduction MOLREP phasing REFMAC refinement