2GDQ

Crystal structure of mandelate racemase/muconate lactonizing enzyme from Bacillus subtilis at 1.8 A resolution


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52940.2M Lithium Sulfate, 0.1M Tris, pH 8.5, 25% w/v PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties
Matthews coefficientSolvent content
2.3247.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.374α = 90
b = 113.246β = 90
c = 168.612γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 165 mmSGX-CAT2006-03-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-ID0.9793APS31-ID

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
11.85097.80.0649.65.27214070561
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)
11.81.8687.487.40.8454

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 REPLACEMENTTHROUGHOUT1MUC1.827.467200070202354896.670.20.20.1970.252RANDOM26.313
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_deg33.491
r_dihedral_angle_4_deg19.608
r_dihedral_angle_3_deg14.496
r_dihedral_angle_1_deg5.778
r_scangle_it3.594
r_scbond_it2.426
r_mcangle_it1.533
r_angle_refined_deg1.436
r_mcbond_it1.029
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.491
r_dihedral_angle_4_deg19.608
r_dihedral_angle_3_deg14.496
r_dihedral_angle_1_deg5.778
r_scangle_it3.594
r_scbond_it2.426
r_mcangle_it1.533
r_angle_refined_deg1.436
r_mcbond_it1.029
r_nbtor_refined0.307
r_symmetry_vdw_refined0.236
r_nbd_refined0.208
r_symmetry_hbond_refined0.185
r_xyhbond_nbd_refined0.175
r_chiral_restr0.097
r_bond_refined_d0.015
r_gen_planes_refined0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5958
Nucleic Acid Atoms
Solvent Atoms741
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
HKL-2000data reduction