5FH0

The structure of rat cytosolic PEPCK variant E89A complex with GTP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3DT2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.429825% PEG 3350, 0.1M HEPES PH 7.4, 8MM MNCL2, 10mM GTP
Crystal Properties
Matthews coefficientSolvent content
2.2144.29

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 60.428α = 90
b = 85.71β = 90
c = 118.415γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRAYONIX MX-3002014-07-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONCLSI BEAMLINE 08ID-10.97949CLSI08ID-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)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
11.610099.20.0660.0680.01816.813.981130
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6692.90.3440.3610.1070.9710.87499

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 REPLACEMENTTHROUGHOUT3DT21.669.4377001405398.470.20230.20070.2316RANDOM30.211
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
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.915
r_dihedral_angle_4_deg13.855
r_dihedral_angle_3_deg12.691
r_dihedral_angle_1_deg6.399
r_mcangle_it2.732
r_mcbond_it1.797
r_mcbond_other1.797
r_angle_refined_deg1.48
r_angle_other_deg0.935
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.915
r_dihedral_angle_4_deg13.855
r_dihedral_angle_3_deg12.691
r_dihedral_angle_1_deg6.399
r_mcangle_it2.732
r_mcbond_it1.797
r_mcbond_other1.797
r_angle_refined_deg1.48
r_angle_other_deg0.935
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4860
Nucleic Acid Atoms
Solvent Atoms393
Heterogen Atoms51

Software

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