4MVA

1.43 Angstrom Resolution Crystal Structure of Triosephosphate Isomerase (tpiA) from Escherichia coli in Complex with Acetyl Phosphate.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1TREPDB ENTRY 1TRE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.5295Protein: 7.4mg/mL, 0.15M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: Classics II (F11), 0.2M Sodium chloride, 0.1M Bis-Tris pH 6.5, 25% (w/v) PEG 3350, 10mM ACP, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9938.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.535α = 90
b = 67.529β = 90
c = 150.336γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDBeryllium lenses2013-03-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-G0.97856APS21-ID-G

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
11.433099.90.06222.76.18865988659-316.2
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)
11.431.451000.5343.464416

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1TRE1.4329.248394683946443399.910.135670.135670.134560.15614RANDOM19.023
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]
-0.090.66-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.623
r_dihedral_angle_4_deg10.242
r_dihedral_angle_3_deg9.701
r_long_range_B_refined6.988
r_long_range_B_other6.384
r_dihedral_angle_1_deg3.588
r_scangle_other3.129
r_scbond_it2.084
r_scbond_other2.084
r_mcangle_other2.044
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.623
r_dihedral_angle_4_deg10.242
r_dihedral_angle_3_deg9.701
r_long_range_B_refined6.988
r_long_range_B_other6.384
r_dihedral_angle_1_deg3.588
r_scangle_other3.129
r_scbond_it2.084
r_scbond_other2.084
r_mcangle_other2.044
r_mcangle_it2.043
r_angle_refined_deg1.471
r_mcbond_it1.261
r_mcbond_other1.258
r_angle_other_deg0.762
r_chiral_restr0.083
r_gen_planes_refined0.017
r_gen_planes_other0.016
r_bond_refined_d0.01
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3780
Nucleic Acid Atoms
Solvent Atoms837
Heterogen Atoms37

Software

Software
Software NamePurpose
Blu-Icedata collection
PHASERphasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling