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Crystal structure of geraniol-NUDX1 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KYX
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 2.51 50.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.761 α = 90 b = 83.582 β = 90 c = 116.36 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 ADSC QUANTUM 315r 2016-04-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U 0.9793 SSRF BL17U
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 1.7 50 99.9 15.8 7.1 75230
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 4KYX 1.702 44.681 1.34 75131 3683 99.82 0.1845 0.1831 0.1865 0.2099 0.2135
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 12.559 f_angle_d 0.866 f_chiral_restr 0.059 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4458 Nucleic Acid Atoms Solvent Atoms 689 Heterogen Atoms
Software Software Software Name Purpose PHENIX refinement HKL-2000 data collection XDS data processing PHASER phasing