3R2E

Dihydroneopterin aldolase/dihydroneopterin triphosphate 2'-epimerase from Yersinia pestis.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2O90 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.52890.2 M calcium chloride, 0.1 M Bis-tris buffer, 45% MPD, 10 mM guanine, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1442.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.716α = 90
b = 71.716β = 90
c = 107.629γ = 90
Symmetry
Space GroupI 4 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 210r2010-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.9792APS19-BM

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
12.153199.60.0612.66.87990799057.7
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)
2.152.191000.8552.055.8395

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 REPLACEMENTTHROUGHOUT2O902.15317960796036899.170.21710.21710.21530.2553RANDOM67.9161
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]
0.450.45-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.248
r_dihedral_angle_3_deg19.889
r_dihedral_angle_4_deg14.711
r_dihedral_angle_1_deg7.881
r_scangle_it4.445
r_scbond_it2.648
r_mcangle_it1.723
r_angle_refined_deg1.698
r_mcbond_it0.927
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.248
r_dihedral_angle_3_deg19.889
r_dihedral_angle_4_deg14.711
r_dihedral_angle_1_deg7.881
r_scangle_it4.445
r_scbond_it2.648
r_mcangle_it1.723
r_angle_refined_deg1.698
r_mcbond_it0.927
r_chiral_restr0.116
r_bond_refined_d0.018
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms922
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
MOLREPphasing
HKL-3000phasing