2WD8 | pdb_00002wd8

PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN COMPLEX WITH NADP AND DDD00071204


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C7VPDB ENTRY 2C7V

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.61.8M NA ACETATE, 0.1M CITRATE BUFFER PH6.0, pH 4.6
Crystal Properties
Matthews coefficientSolvent content
2.0339

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.64α = 90
b = 89.801β = 115.55
c = 83.061γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMIRRORS2007-08-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007

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
12.13084.70.0913.52.448991
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)
12.12.1884.90.562.42.3

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2C7V2.13046474249684.410.161870.158440.160.226220.23RANDOM32.285
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]
-2.74-1.143.38-1.63
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.52
r_dihedral_angle_4_deg18.371
r_dihedral_angle_3_deg16.289
r_dihedral_angle_1_deg5.795
r_scangle_it2.541
r_scbond_it1.687
r_angle_refined_deg1.419
r_mcangle_it1.01
r_mcbond_it0.615
r_nbtor_refined0.297
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7410
Nucleic Acid Atoms
Solvent Atoms733
Heterogen Atoms246

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing