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Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with propylthio-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 8.5 295 Protein (15 mg/mL); Reservoir (0.17 M sodium acetate, 85 mM Tris:HCl (pH 8.5), 25% (w/v) PEG 4000 and 15% (v/v) glycerol)
Crystal Properties Matthews coefficient Solvent content 2.92 57.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 122.76 α = 90 b = 122.76 β = 90 c = 44.484 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 2014-09-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.075 NSLS X29A
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 1.48 50 100 0.079 0.083 0.024 10.2 11.5 64277 11.9
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.48 1.51 100 0.876 0.825 3 10.7
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 1.48 25 61028 3177 99.93 0.168 0.1671 0.1665 0.1849 0.1843 RANDOM 19.003
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] 0.08 0.04 0.08 -0.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.087 r_dihedral_angle_4_deg 14.326 r_dihedral_angle_3_deg 13.004 r_dihedral_angle_1_deg 5.656 r_mcangle_it 1.698 r_scbond_it 1.49 r_angle_refined_deg 1.432 r_mcbond_it 0.983 r_chiral_restr 0.075 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.087 r_dihedral_angle_4_deg 14.326 r_dihedral_angle_3_deg 13.004 r_dihedral_angle_1_deg 5.656 r_mcangle_it 1.698 r_scbond_it 1.49 r_angle_refined_deg 1.432 r_mcbond_it 0.983 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2105 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 35
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction