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Crystal structure of double mutant E. Coli purine nucleoside phosphorylase with 4 FMC molecules
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1K9S PDB entry 1k9s
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.2 291 50 mM citric buffer, 34 % ammonium sulphate
Crystal Properties Matthews coefficient Solvent content 2.4 47.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.933 α = 90 b = 124.174 β = 90 c = 189.436 γ = 90
Symmetry Space Group P 21 21 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 MAR CCD 165 mm 2012-03-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM14 0.97977 ESRF BM14
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim 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 1.89 47.8 98.7 0.169 0.184 10.89 6.5 757830 116237 -3 26.915
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.89 2 92.3 1.212 1.368 1.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 FREE R-VALUE PDB entry 1k9s 1.89 47.7 1.99 116136 5807 98.76 0.1688 0.1666 0.1662 0.2103 0.2098 random 21.377
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]
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 14.178 f_angle_d 1.168 f_chiral_restr 0.075 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 10624 Nucleic Acid Atoms Solvent Atoms 1247 Heterogen Atoms 131
Software Software Software Name Purpose XSCALE data scaling PDB_EXTRACT data extraction PHENIX refinement XDS data reduction