2IFC

The Structure of the Binary Complex of Oxalateacetate with Citrate Synthase from the Thermophilic Archaeon Thermolasma acidophilum


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1O7X1O7X_A

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.528017 % PEG 4000, 100mM Hepes 8.5, 200mM Sodium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 280K
Crystal Properties
Matthews coefficientSolvent content
2.3748.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 78.526α = 90
b = 97.447β = 93.1
c = 106.937γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDNOIR-1Double crystal2006-07-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 4.2.21.0000ALS4.2.2

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
11.741.3896.80.09106.19170739170738
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)
11.71.7694.50.482.96.0316592

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1O7X_A1.741.38170707170707856096.770.1830.1810.234RANDOM26.348
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]
-0.17-0.050.110.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.618
r_dihedral_angle_4_deg15.864
r_dihedral_angle_3_deg14.959
r_dihedral_angle_1_deg5.562
r_scangle_it3.921
r_scbond_it2.619
r_angle_refined_deg1.602
r_mcangle_it1.563
r_mcbond_it1.108
r_nbtor_refined0.306
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.618
r_dihedral_angle_4_deg15.864
r_dihedral_angle_3_deg14.959
r_dihedral_angle_1_deg5.562
r_scangle_it3.921
r_scbond_it2.619
r_angle_refined_deg1.602
r_mcangle_it1.563
r_mcbond_it1.108
r_nbtor_refined0.306
r_nbd_refined0.211
r_symmetry_hbond_refined0.187
r_symmetry_vdw_refined0.182
r_xyhbond_nbd_refined0.166
r_chiral_restr0.121
r_bond_refined_d0.02
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11958
Nucleic Acid Atoms
Solvent Atoms2228
Heterogen Atoms36

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
d*TREKdata scaling
PDB_EXTRACTdata extraction
CNSphasing