4E2B

High resolution crystal structure of the old yellow enzyme from Trypanosoma cruzi


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3ATYPDB ENTRY 3ATY

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP829228% (w/v) polyethylene glycol 1500 and 0.3 M ammonium fluoride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
1.9737.57

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 57.347α = 90
b = 68.656β = 90
c = 85.19γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2011-10-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONLNLS BEAMLINE W01B-MX21.46LNLSW01B-MX2

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
11.2693098.30.0474.91050318792212
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)
11.2691.3299.90.5224.6

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3ATY1.26922.488792283454440998.30.147180.145920.17084RANDOM14.677
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]
-1.29-0.251.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.749
r_dihedral_angle_4_deg16.442
r_sphericity_free11.695
r_dihedral_angle_3_deg11.613
r_sphericity_bonded6.726
r_dihedral_angle_1_deg5.879
r_rigid_bond_restr1.784
r_angle_refined_deg1.161
r_chiral_restr0.079
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.749
r_dihedral_angle_4_deg16.442
r_sphericity_free11.695
r_dihedral_angle_3_deg11.613
r_sphericity_bonded6.726
r_dihedral_angle_1_deg5.879
r_rigid_bond_restr1.784
r_angle_refined_deg1.161
r_chiral_restr0.079
r_bond_refined_d0.005
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2965
Nucleic Acid Atoms
Solvent Atoms363
Heterogen Atoms70

Software

Software
Software NamePurpose
NatXraydata collection
MOLREPphasing
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling