2PTZ

Crystal Structure of the T. brucei enolase complexed with phosphonoacetohydroxamate (PAH), His156-out conformation


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.529110 % (w/v) PEG1000, 0.01 M ZnSO4 or ZnCl2, and 0.1 M MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 73.858α = 90
b = 109.279β = 90
c = 107.946γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmMIRRORS2003-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE D03B-MX11.42LNLSD03B-MX1

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
11.652895.50.05526.48.3525805021411
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)
1.651.7491.40.4093.98.3

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 REPLACEMENTTHROUGHOUT1OEP1.6527.955006447566255495.010.166920.165010.20344RANDOM29.621
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]
-0.07-0.050.12
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.818
r_dihedral_angle_4_deg19.007
r_dihedral_angle_3_deg13.583
r_dihedral_angle_1_deg6.565
r_scangle_it4.628
r_scbond_it2.918
r_mcangle_it2.342
r_angle_refined_deg1.668
r_mcbond_it1.501
r_nbtor_refined0.312
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.818
r_dihedral_angle_4_deg19.007
r_dihedral_angle_3_deg13.583
r_dihedral_angle_1_deg6.565
r_scangle_it4.628
r_scbond_it2.918
r_mcangle_it2.342
r_angle_refined_deg1.668
r_mcbond_it1.501
r_nbtor_refined0.312
r_symmetry_vdw_refined0.22
r_nbd_refined0.211
r_symmetry_hbond_refined0.178
r_xyhbond_nbd_refined0.148
r_chiral_restr0.106
r_metal_ion_refined0.072
r_symmetry_metal_ion_refined0.023
r_bond_refined_d0.017
r_gen_planes_refined0.008
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3288
Nucleic Acid Atoms
Solvent Atoms421
Heterogen Atoms16

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing