2YIM

The enolisation chemistry of a thioester-dependent racemase: the 1.4 A crystal structure of a complex with a planar reaction intermediate analogue


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GCEPDB ENTRY 2GCE

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
171.52 M AMMONIUM PHOSPHATE PH 7.0, 10 MM BACL2.
Crystal Properties
Matthews coefficientSolvent content
2.6753.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 181.59α = 90
b = 80.17β = 91.41
c = 118.88γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4MIRRORS2008-11-13MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.4121.398.70.0611.93.632276012.2
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)
11.411.4996.90.482.43.5

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 2GCE1.41118.843064691629098.570.187070.186150.2046RANDOM15.115
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]
0.040.040.1-0.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.846
r_dihedral_angle_4_deg15.011
r_dihedral_angle_3_deg12.743
r_dihedral_angle_1_deg4.881
r_scangle_it1.574
r_angle_refined_deg1.065
r_scbond_it0.965
r_mcangle_it0.703
r_mcbond_it0.376
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.846
r_dihedral_angle_4_deg15.011
r_dihedral_angle_3_deg12.743
r_dihedral_angle_1_deg4.881
r_scangle_it1.574
r_angle_refined_deg1.065
r_scbond_it0.965
r_mcangle_it0.703
r_mcbond_it0.376
r_chiral_restr0.073
r_bond_refined_d0.006
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
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 Atoms10731
Nucleic Acid Atoms
Solvent Atoms1818
Heterogen Atoms260

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling