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Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with methylthio-DADMe-Immucillin-A
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 5.5 295 Protein (15 mg/mL); Reservoir (0.2 M magnesium chloride, 0.1 M sodium citrate:citric acid (pH 5.5) and 40% (v/v) PEG 400)
Crystal Properties Matthews coefficient Solvent content 2.95 58.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.065 α = 90 b = 123.065 β = 90 c = 44.755 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 ADSC QUANTUM 315r 2014-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.54178 NSLS X29A
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 1.8 50 99.5 0.085 11.6 6.4 36094 13
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 1.8 1.83 94 0.563 2.61 4.4
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 1.8 25 34254 1832 99.5 0.1612 0.1602 0.1728 0.1804 0.1894 RANDOM 19.439
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] -0.54 -0.27 -0.54 1.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.607 r_dihedral_angle_4_deg 18.137 r_dihedral_angle_3_deg 12.431 r_dihedral_angle_1_deg 5.791 r_mcangle_it 1.766 r_angle_refined_deg 1.504 r_mcbond_it 1.103 r_mcbond_other 1.086 r_angle_other_deg 0.926 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.607 r_dihedral_angle_4_deg 18.137 r_dihedral_angle_3_deg 12.431 r_dihedral_angle_1_deg 5.791 r_mcangle_it 1.766 r_angle_refined_deg 1.504 r_mcbond_it 1.103 r_mcbond_other 1.086 r_angle_other_deg 0.926 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 2109 Nucleic Acid Atoms Solvent Atoms 185 Heterogen Atoms 70
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction