2XH7

Engineering the enolase active site pocket: Crystal structure of the D321A mutant of yeast enolase 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2XH4PDB ENTRY 2XH4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1818% PEG 6000, 0.2M MAGNESIUM CHLORIDE, 0.1M TRIS PH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.2745.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 61.973α = 67.89
b = 62β = 78.33
c = 64.32γ = 80.6
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2009-07-27MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SASLSX10SA

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
11.85091.30.1511.431.8173622226.5
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)
11.81.9189.60.683.121.75

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 REPLACEMENTTHROUGHOUTPDB ENTRY 2XH41.843.6970010370791.60.1770.1750.214RANDOM20.06
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_deg34.724
r_dihedral_angle_4_deg15.368
r_dihedral_angle_3_deg12.961
r_dihedral_angle_1_deg5.399
r_scangle_it2.1
r_scbond_it1.304
r_angle_refined_deg1.071
r_mcangle_it0.848
r_mcbond_it0.506
r_nbtor_refined0.299
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.724
r_dihedral_angle_4_deg15.368
r_dihedral_angle_3_deg12.961
r_dihedral_angle_1_deg5.399
r_scangle_it2.1
r_scbond_it1.304
r_angle_refined_deg1.071
r_mcangle_it0.848
r_mcbond_it0.506
r_nbtor_refined0.299
r_nbd_refined0.229
r_symmetry_vdw_refined0.15
r_symmetry_hbond_refined0.129
r_xyhbond_nbd_refined0.104
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.003
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_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6470
Nucleic Acid Atoms
Solvent Atoms747
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing