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Crystal structure of purine nucleoside phosphorylase from Meiothermus ruber DSM 1279, NYSGRC Target 029804.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 0.1 M Magnesium Chloride, 0.1 M MES:NaOH, pH 6.5, 30%
PEG 400, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.4 48.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 56.629 α = 90 b = 188.93 β = 90 c = 153.002 γ = 90
Symmetry Space Group C 2 2 21
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 2013-07-21 SAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9791 APS 31-ID
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 1.6 50 99.7 0.107 8.4 13.2 107774
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 1.6 1.63 96.1 0.995 11.6 5124
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD THROUGHOUT 1.6 31.26 107668 5372 99.6 0.204 0.203 0.2027 0.221 0.2211 RANDOM 30.7939
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] 47.12 -19.81 -27.31
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.715 r_dihedral_angle_4_deg 15.922 r_dihedral_angle_3_deg 13.041 r_dihedral_angle_1_deg 5.764 r_mcangle_it 2.338 r_scbond_it 2.144 r_mcbond_it 1.393 r_angle_refined_deg 1.364 r_chiral_restr 0.086 r_bond_refined_d 0.008
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.715 r_dihedral_angle_4_deg 15.922 r_dihedral_angle_3_deg 13.041 r_dihedral_angle_1_deg 5.764 r_mcangle_it 2.338 r_scbond_it 2.144 r_mcbond_it 1.393 r_angle_refined_deg 1.364 r_chiral_restr 0.086 r_bond_refined_d 0.008 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5361 Nucleic Acid Atoms Solvent Atoms 453 Heterogen Atoms 11
Software Software Software Name Purpose SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction SHELXS phasing