5FH5

The structure of rat cytosolic PEPCK variant E89Q in complex with phosphoglycolate and GDP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QEY 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429825% PEG 3350, 0.1M HEPES PH 7.4, 8MM MNCL2, 10mM GDP
Crystal Properties
Matthews coefficientSolvent content
2.3146.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.176α = 90
b = 119.717β = 107.29
c = 60.897γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2011-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL7-10.97SSRLBL7-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.5510098.30.06513.75.890078
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.551.6196.40.41158821

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 REPLACEMENTTHROUGHOUT2QEY1.5535.585515450897.960.20980.20830.2369RANDOM34.592
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]
0.570.36-0.74-0.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.097
r_dihedral_angle_4_deg16.014
r_dihedral_angle_3_deg13.135
r_dihedral_angle_1_deg6.628
r_angle_refined_deg1.775
r_mcangle_it1.128
r_angle_other_deg1.018
r_mcbond_it0.664
r_mcbond_other0.663
r_chiral_restr0.103
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.097
r_dihedral_angle_4_deg16.014
r_dihedral_angle_3_deg13.135
r_dihedral_angle_1_deg6.628
r_angle_refined_deg1.775
r_mcangle_it1.128
r_angle_other_deg1.018
r_mcbond_it0.664
r_mcbond_other0.663
r_chiral_restr0.103
r_bond_refined_d0.016
r_gen_planes_refined0.01
r_bond_other_d0.004
r_gen_planes_other0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4798
Nucleic Acid Atoms
Solvent Atoms664
Heterogen Atoms68

Software

Software
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction
MOLREPphasing