4K6A

Revised Crystal Structure of apo-form of Triosephosphate Isomerase (tpiA) from Escherichia coli at 1.8 Angstrom Resolution.


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8295Protein: 7.6mg/mL, 0.5M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: PACT (D11), 0.2M Calcium chloride, 0.1M Tris-HCl pH 8.0, 20% (w/v) PEG 6000., VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties
Matthews coefficientSolvent content
1.9637.13

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.066α = 90
b = 67.488β = 90
c = 149.769γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 300 mm CCDMirrors2013-03-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 21-ID-D1.03326APS21-ID-D

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
11.83099.90.08818.35.84423144231-318.5
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)
11.81.8398.40.5292.64.12158

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 REPLACEMENTTHROUGHOUT1TRE1.829.064190641906222899.850.150750.150750.148950.1847RANDOM16.865
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]
0.02-0.160.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.452
r_dihedral_angle_4_deg10.237
r_dihedral_angle_3_deg9.469
r_scangle_it4.664
r_scbond_it2.815
r_dihedral_angle_1_deg2.769
r_mcangle_it1.584
r_angle_refined_deg1.327
r_mcbond_it0.973
r_angle_other_deg0.878
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.452
r_dihedral_angle_4_deg10.237
r_dihedral_angle_3_deg9.469
r_scangle_it4.664
r_scbond_it2.815
r_dihedral_angle_1_deg2.769
r_mcangle_it1.584
r_angle_refined_deg1.327
r_mcbond_it0.973
r_angle_other_deg0.878
r_mcbond_other0.329
r_chiral_restr0.08
r_bond_refined_d0.012
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3786
Nucleic Acid Atoms
Solvent Atoms546
Heterogen Atoms1

Software

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