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Crystal structure of a sugar kinase (Target EFI-502132) from Oceanicola granulosus with bound AMP, crystal form II
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LHX PDB ENTRY 3LHX
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SITTING DROP, VAPOR DIFFUSION 4 298 protein (10 mM HEPES, pH 7.5, 150 mM sodium chloride, 10% glycerol, 1 mM DTT, 5 mM AMP-PNP), reservoir (0.2 M magnesium chloride, 0.1 M Bis-Tris, pH 6.5, 25% PEG3350), cryoprotectant (reservoir + 20% glycerol), SITTING DROP, VAPOR DIFFUSION, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.32 47.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.54 α = 90 b = 49.528 β = 101.5 c = 83.267 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 RAYONIX MX225HE MIRRORS 2012-02-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.8 81.595 95.8 0.08 8.8 3.4 56642 56642
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.9 95.9 0.645 0.645 1.2 3.2 8243
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB ENTRY 3LHX 1.8 27.198 1.33 56598 56598 2847 95.46 0.1786 0.1763 0.1763 0.2207 0.2166 RANDOM 31.5299
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] -2.6208 -1.2618 4.3788 -1.758
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 13.903 f_angle_d 1.109 f_chiral_restr 0.074 f_bond_d 0.007 f_plane_restr 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4420 Nucleic Acid Atoms Solvent Atoms 426 Heterogen Atoms 51
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction PHENIX phasing