☰ Navigation Tabs
Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with 5'-methylthiotubercidin at 1.75 angstrom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K27
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 295 Protein (15 mg/mL); Reservoir (0.2 M lithium sulfate, 0.1 M TRIS pH 8.5 and 20% (w/v) PEG 4000)
Crystal Properties Matthews coefficient Solvent content 2.95 58.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.359 α = 90 b = 123.359 β = 90 c = 44.499 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 2015-02-13 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) 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 1.74 50 99.4 0.083 0.087 18.64 11.07 39581 -3 29.869
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.74 1.85 98.5 0.729 0.765 3.09 11.13
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 1K27 1.75 25 37326 1965 99.59 0.1702 0.1695 0.1798 0.1843 0.1959 RANDOM 27.994
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] 0.49 0.25 0.49 -1.61
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.519 r_dihedral_angle_4_deg 14.658 r_dihedral_angle_3_deg 13.74 r_dihedral_angle_1_deg 6.125 r_mcangle_it 2.917 r_mcbond_it 1.768 r_mcbond_other 1.766 r_angle_refined_deg 1.461 r_angle_other_deg 0.957 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.519 r_dihedral_angle_4_deg 14.658 r_dihedral_angle_3_deg 13.74 r_dihedral_angle_1_deg 6.125 r_mcangle_it 2.917 r_mcbond_it 1.768 r_mcbond_other 1.766 r_angle_refined_deg 1.461 r_angle_other_deg 0.957 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2096 Nucleic Acid Atoms Solvent Atoms 189 Heterogen Atoms 36
Software Software Software Name Purpose XDS data reduction XDS data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction