2O56 | pdb_00002o56

Crystal Structure of a Member of the Enolase Superfamily from Salmonella Typhimurium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2GL5pdb entry 2GL5

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7294100MM DL-MALEIC ACID, 25% PEG 3350, 50MM MGCL2, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K, pH 7.00
Crystal Properties
Matthews coefficientSolvent content
2.5852.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 107.662α = 90
b = 140.818β = 105.94
c = 126.838γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMIRRORS2006-12-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 31-IDAPS31-ID

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
125098.60.0830.0725.43.424182424182429
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
122.0796.80.460.411.93.123617

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTpdb entry 2GL5220231877231877475796.840.209790.208870.210.255310.25RANDOM33.287
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]
3.010.57-1.24-1.45
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.48
r_dihedral_angle_4_deg20.343
r_dihedral_angle_3_deg16.284
r_scangle_it8.978
r_dihedral_angle_1_deg7.364
r_scbond_it6.93
r_mcangle_it5.402
r_mcbond_it4.476
r_angle_refined_deg1.249
r_symmetry_hbond_refined0.322
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.48
r_dihedral_angle_4_deg20.343
r_dihedral_angle_3_deg16.284
r_scangle_it8.978
r_dihedral_angle_1_deg7.364
r_scbond_it6.93
r_mcangle_it5.402
r_mcbond_it4.476
r_angle_refined_deg1.249
r_symmetry_hbond_refined0.322
r_nbtor_refined0.311
r_symmetry_vdw_refined0.235
r_xyhbond_nbd_refined0.198
r_nbd_refined0.184
r_chiral_restr0.108
r_bond_refined_d0.01
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms24220
Nucleic Acid Atoms
Solvent Atoms1808
Heterogen Atoms8

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling