3UWZ

Crystal structure of Staphylococcus aureus triosephosphate isomerase complexed with glycerol-2-phosphate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3M9YPDB ENTRY 3M9Y

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52981.6M TRISODIUM CITRATE, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.4249.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 79.022α = 90
b = 79.022β = 90
c = 174.956γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++MIRROR2010-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.49772.01799.50.08627.41419971
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)
12.52.63990.5240.5241.513.9

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 3M9Y2.529.6618891101699.40.1920.190.233RANDOM39.67
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]
1.581.58-3.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.158
r_dihedral_angle_3_deg13.833
r_dihedral_angle_4_deg9.756
r_dihedral_angle_1_deg4.671
r_scangle_it4.121
r_scbond_it2.298
r_angle_refined_deg0.979
r_mcangle_it0.809
r_mcbond_it0.382
r_chiral_restr0.062
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.158
r_dihedral_angle_3_deg13.833
r_dihedral_angle_4_deg9.756
r_dihedral_angle_1_deg4.671
r_scangle_it4.121
r_scbond_it2.298
r_angle_refined_deg0.979
r_mcangle_it0.809
r_mcbond_it0.382
r_chiral_restr0.062
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3815
Nucleic Acid Atoms
Solvent Atoms147
Heterogen Atoms25

Software

Software
Software NamePurpose
StructureStudiodata collection
MOLREPphasing
REFMACrefinement
XDSdata reduction
SCALAdata scaling