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Crystal Structure of Xanthosine monophosphate phosphatase in the unliganded state
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ONN 3ONN, 3NUQ, 3OPX experimental model PDB 3NUQ 3ONN, 3NUQ, 3OPX experimental model PDB 3OPX 3ONN, 3NUQ, 3OPX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.1M Tris (pH 8.5) 20%(w/v) PEG6000
Crystal Properties Matthews coefficient Solvent content 2.1 41.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 37.063 α = 90 b = 55.276 β = 93.862 c = 57.154 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 270 2017-09-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 7A (6B, 6C1) 0.97933 PAL/PLS 7A (6B, 6C1)
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 1.34 50 98.9 0.993 31.1 5.4 51330 16.3914703102
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 1.34 1.39 96.9 0.273 0.948 4.9
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) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 3ONN, 3NUQ, 3OPX 1.34 27.638 1.35126352174 51239 2006 99.083402626 0.191001893214 0.189576113012 0.1908 0.226342603108 0.2263 23.3574282507
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 12.8834235965 f_angle_d 1.41539893955 f_chiral_restr 0.0669994277494 f_bond_d 0.0124070688428 f_plane_restr 0.00907858245176
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1828 Nucleic Acid Atoms Solvent Atoms 192 Heterogen Atoms 1
Software Software Software Name Purpose PHENIX refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing