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Crystal Structure of human 5'-deoxy-5'-methyladenosine phosphorylase in complex with pCl-phenylthioDADMeImmA
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.2 291 0.2M NaCl, 0.1M phosphate buffer, 10% PEG 8000, pH 6.2, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 3.15 60.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.252 α = 90 b = 123.252 β = 90 c = 44.879 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 2010-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X29A 1.0809 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 1.93 50 99.5 0.077 11.1 7.2 29552
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 1.93 2 94.8 0.376 7 2754
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1.93 50 29481 1562 99.57 0.1318 0.1305 0.1541 0.1599 RANDOM 21.5879
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] -3.2 -3.2 6.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.227 r_dihedral_angle_4_deg 19.784 r_dihedral_angle_3_deg 15.959 r_dihedral_angle_1_deg 5.899 r_scangle_it 3.878 r_scbond_it 2.343 r_angle_refined_deg 1.459 r_mcangle_it 1.418 r_mcbond_it 0.779 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.227 r_dihedral_angle_4_deg 19.784 r_dihedral_angle_3_deg 15.959 r_dihedral_angle_1_deg 5.899 r_scangle_it 3.878 r_scbond_it 2.343 r_angle_refined_deg 1.459 r_mcangle_it 1.418 r_mcbond_it 0.779 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2112 Nucleic Acid Atoms Solvent Atoms 67 Heterogen Atoms 31
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction