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1.9 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with Glycerol.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EZW
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 1:1 v/v protein solution [10mg/ml protein, 0.3M NaCl, 10mM Na Hepes pH 7.5), screen solution (0.2M Na dihydrogen Phosphate , 20% PEG 3350, 6% Glycerol), VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.44 49.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.75 α = 90 b = 193.742 β = 103.6 c = 91.669 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 300 mm CCD 2008-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 21-ID-D 0.98400 APS 21-ID-D
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 1.9 50 100 0.081 15.6 3.9 168279 168279 -3 23.4
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 1.9 1.93 100 0.494 2.9 3.8 8395
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 THROUGHOUT 3EZW 1.9 44.81 159730 159730 8479 99.85 0.19529 0.19529 0.19266 0.2096 0.24562 0.2601 RANDOM 15.064
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] 4.41 0.58 -2.76 -1.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.732 r_dihedral_angle_4_deg 14.063 r_dihedral_angle_3_deg 12.183 r_scangle_it 5.319 r_dihedral_angle_1_deg 4.128 r_scbond_it 3.723 r_mcangle_it 2.175 r_angle_refined_deg 1.679 r_mcbond_it 1.471 r_angle_other_deg 0.971
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.732 r_dihedral_angle_4_deg 14.063 r_dihedral_angle_3_deg 12.183 r_scangle_it 5.319 r_dihedral_angle_1_deg 4.128 r_scbond_it 3.723 r_mcangle_it 2.175 r_angle_refined_deg 1.679 r_mcbond_it 1.471 r_angle_other_deg 0.971 r_mcbond_other 0.547 r_chiral_restr 0.107 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_gen_planes_other 0.002 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 15703 Nucleic Acid Atoms Solvent Atoms 1174 Heterogen Atoms 96
Software Software Software Name Purpose Blu-Ice data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling