2XH0

Engineering the enolase active site pocket: Crystal structure of the S39N Q167K D321R mutant of yeast enolase 1


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ONEPDB ENTRY 2ONE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.625% PEG 4000, 0.1M SODIUM ACETATE PH 4.6
Crystal Properties
Matthews coefficientSolvent content
1.9336.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 55.329α = 89.89
b = 60.797β = 89.9
c = 120.667γ = 65.84
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2008-09-07MSINGLE 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
11.740930.169.691.97147095222.3
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)
11.71.886.90.772.341.67

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 2ONE1.737.85139807741193.20.1990.1970.246RANDOM15.41
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_deg38.048
r_dihedral_angle_4_deg16.566
r_dihedral_angle_3_deg14.106
r_dihedral_angle_1_deg6.064
r_scangle_it2.793
r_scbond_it1.835
r_angle_refined_deg1.315
r_mcangle_it1.074
r_mcbond_it0.691
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.048
r_dihedral_angle_4_deg16.566
r_dihedral_angle_3_deg14.106
r_dihedral_angle_1_deg6.064
r_scangle_it2.793
r_scbond_it1.835
r_angle_refined_deg1.315
r_mcangle_it1.074
r_mcbond_it0.691
r_nbtor_refined0.304
r_symmetry_vdw_refined0.267
r_nbd_refined0.217
r_symmetry_hbond_refined0.204
r_xyhbond_nbd_refined0.151
r_chiral_restr0.095
r_bond_refined_d0.011
r_gen_planes_refined0.005
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 Atoms13123
Nucleic Acid Atoms
Solvent Atoms1569
Heterogen Atoms44

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
MOLREPphasing