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Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with 2-amino-MTA and sulfate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K27 PDB entry 1K27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 Protein 15 mg/mL, Reservoir 0.2 M magnesium chloride, 20% (w/v) PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.92 57.82
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 121.504 α = 90 b = 121.504 β = 90 c = 45.328 γ = 120
Symmetry Space Group P 3 2 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 RAYONIX MX225HE 2015-07-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.97931 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.8 50 98.7 0.091 0.099 0.038 9.5 6 35008 25
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 1.8 1.83 99.8 0.738 0.809 0.325 0.874 2.27 5.9 1719
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1K27 1.81 25 33251 1701 98.47 0.1703 0.1691 0.1827 0.1928 0.2043 RANDOM 25.86
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] -1.14 -0.57 -1.14 3.7
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.001 r_dihedral_angle_4_deg 13.47 r_dihedral_angle_3_deg 12.521 r_dihedral_angle_1_deg 6.1 r_mcangle_it 2.184 r_angle_refined_deg 1.456 r_mcbond_it 1.435 r_mcbond_other 1.433 r_angle_other_deg 0.922 r_chiral_restr 0.073
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.001 r_dihedral_angle_4_deg 13.47 r_dihedral_angle_3_deg 12.521 r_dihedral_angle_1_deg 6.1 r_mcangle_it 2.184 r_angle_refined_deg 1.456 r_mcbond_it 1.435 r_mcbond_other 1.433 r_angle_other_deg 0.922 r_chiral_restr 0.073 r_bond_refined_d 0.009 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2072 Nucleic Acid Atoms Solvent Atoms 180 Heterogen Atoms 44
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction