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Crystal structure of AtNUDX1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5GP0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 291.15 Sodium acetate trihydrate, PEG 2000, Ammonium sulfate
Crystal Properties Matthews coefficient Solvent content 2.49 50.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 34.522 α = 90 b = 83.181 β = 90 c = 115.224 γ = 90
Symmetry Space Group P 2 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 DECTRIS PILATUS 6M 2015-12-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL19U1 0.9785 SSRF BL19U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.356 41.59 99.9 25.8 6.3 458092
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 5GP0 1.386 39.12 1.34 67894 3381 99.27 0.1758 0.1757 0.1769 0.1774 0.1789
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 14.537 f_angle_d 1.119 f_chiral_restr 0.086 f_bond_d 0.011 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2200 Nucleic Acid Atoms Solvent Atoms 383 Heterogen Atoms 35
Software Software Software Name Purpose PHENIX refinement HKL-3000 data collection XDS data scaling PHASER phasing