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Nucleotide-bound closed form of a putative sugar kinase MK0840 from Methanopyrus kandleri
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4BGA PDB ENTRY 4BGA CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.6 0.14 M CACL2, 0.07 M SODIUM ACETATE PH 4.6, 10 % ISOPROPANOL AND 28% GLYCEROL
Crystal Properties Matthews coefficient Solvent content 2.3 46.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.79 α = 90 b = 108.54 β = 90 c = 117.35 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 MARMOSAIC 225 mm CCD 2011-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA SLS X06DA
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 1.34 45.2 98.3 0.04 21.12 4.5 154630 2 14.8
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 1.34 1.37 93.2 0.65 2.61 4
Refinement Statistics Diffraction ID Structure Solution 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 PDB ENTRY 4BGA CHAIN A 1.34 45.147 1.99 154611 7732 98.34 0.1588 0.1576 0.1593 0.1828 0.1832 27.09
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] -5.1011 -2.3404 7.4415
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 12.499 f_angle_d 1.482 f_chiral_restr 0.077 f_bond_d 0.012 f_plane_restr 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4798 Nucleic Acid Atoms Solvent Atoms 519 Heterogen Atoms 105
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing