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Nucleotide-bound open 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 4BG8 PDB ENTRY 4BG8 CHAIN A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 MIXED WITH 5 MM ADP, 10 MM MACL2, CRYSTALLIZED IN 0.2 M POTASSIUM SODIUM TARTRATE AND 20% PEG 3350, pH 7.5
Crystal Properties Matthews coefficient Solvent content 2.37 48.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.57 α = 90 b = 111.67 β = 89.55 c = 87.88 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 MARMOSAIC 225 mm CCD 2010-10-06 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 2.6 73.6 100 0.08 21.95 7.6 54893 4 33.99
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 2.6 2.76 100 0.36 5.98 7.69
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 4BG8 CHAIN A 2.6 73.568 2 43757 2188 99.98 0.1569 0.1542 0.208 0.1817 40.44
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 20.379 f_angle_d 1.181 f_chiral_restr 0.065 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9611 Nucleic Acid Atoms Solvent Atoms 222 Heterogen Atoms 213
Software Software Software Name Purpose PHENIX refinement XDS data reduction XDS data scaling PHASER phasing