3EZW

Crystal Structure of a Hyperactive Escherichia coli Glycerol Kinase Mutant Gly230 --> Asp Obtained Using Microfluidic Crystallization Devices


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GLFpdb entry 1GLF

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1microfluidic free interface diffusion8.529820% PEG 1500, 0.3 M MAGNESIUM CHLORIDE, 0.1 M TRIS-HCL, pH 8.5, microfluidic free interface diffusion, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.3447.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 91.116α = 90
b = 114.26β = 91.15
c = 212.624γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 42006-02-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL11-30.97SSRLBL11-3

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
1250840.05936.85.9250186
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0573.20.2256.63.4

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 1GLF220246407503284.050.16790.166730.22478RANDOM24.437
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]
-2.230.590.971.29
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.247
r_dihedral_angle_4_deg19.763
r_dihedral_angle_3_deg15.477
r_dihedral_angle_1_deg7.024
r_scangle_it4.689
r_scbond_it2.989
r_angle_refined_deg1.893
r_mcangle_it1.872
r_angle_other_deg1.673
r_mcbond_it1.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.247
r_dihedral_angle_4_deg19.763
r_dihedral_angle_3_deg15.477
r_dihedral_angle_1_deg7.024
r_scangle_it4.689
r_scbond_it2.989
r_angle_refined_deg1.893
r_mcangle_it1.872
r_angle_other_deg1.673
r_mcbond_it1.107
r_mcbond_other0.338
r_chiral_restr0.116
r_bond_refined_d0.024
r_gen_planes_refined0.01
r_gen_planes_other0.003
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms31113
Nucleic Acid Atoms
Solvent Atoms1526
Heterogen Atoms133

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing