2WD8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2C7V2.13046474249684.410.161870.158440.22622RANDOM32.285
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
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
r_symmetry_vdw_refined0.245
r_nbd_refined0.218
r_xyhbond_nbd_refined0.185
r_symmetry_hbond_refined0.161
r_chiral_restr0.086
r_bond_refined_d0.012
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
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