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Structural analysis of thermostable S. solfataricus purine-specific nucleoside hydrolase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2MAS pdb entry 2MAS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 100 mM HEPES, 5% PEG 3350, 5 mM CaCl2, 5 mM CdCl2, 5 mM MgCl2, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.42 49.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.76 α = 90 b = 81.13 β = 100.7 c = 98.02 γ = 90
Symmetry Space Group P 1 21 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 210 2009-04-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-1 0.933 ESRF ID14-1
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 1.8 100 99.1 0.087 14.69 119836 119836 -3 -3 25.395
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 1.9 98.5 0.619 2.89
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 pdb entry 2MAS 1.8 96.23 119835 119835 6036 99.1 0.172 0.172 0.1698 0.1795 0.2136 0.2213 RANDOM 26.1757
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] -1.57 0.24 0.6 1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.697 r_dihedral_angle_4_deg 16.358 r_dihedral_angle_3_deg 13.18 r_dihedral_angle_1_deg 6.522 r_scangle_it 3.282 r_scbond_it 2.156 r_angle_refined_deg 1.476 r_mcangle_it 1.355 r_angle_other_deg 0.932 r_mcbond_it 0.796
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.697 r_dihedral_angle_4_deg 16.358 r_dihedral_angle_3_deg 13.18 r_dihedral_angle_1_deg 6.522 r_scangle_it 3.282 r_scbond_it 2.156 r_angle_refined_deg 1.476 r_mcangle_it 1.355 r_angle_other_deg 0.932 r_mcbond_it 0.796 r_mcbond_other 0.239 r_chiral_restr 0.091 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9660 Nucleic Acid Atoms Solvent Atoms 961 Heterogen Atoms 136
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction DNA data collection XDS data reduction