4CM8

Crystal structure of pteridine reductase 1 (PTR1) from Trypanosoma brucei in ternary complex with cofactor and inhibitor


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1RESERVOIR CONTAINED 1.7-2.7 M SODIUM ACETATE, 20-50 MM SODIUM CITRATE PH 4.5-5.0
Crystal Properties
Matthews coefficientSolvent content
2.0439.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.6α = 90
b = 90β = 115.57
c = 82.6γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944 HG2012-04-30MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
11.915.5592.30.0613.93.771435
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)
11.92800.174.82.3

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 2C7V1.915.567827357691.950.144020.141490.19182RANDOM14.892
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]
-1.01-0.482.06-0.56
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.947
r_dihedral_angle_4_deg18.953
r_dihedral_angle_3_deg13.554
r_dihedral_angle_1_deg6.157
r_mcangle_it2.011
r_scbond_it1.757
r_angle_refined_deg1.72
r_mcbond_it1.208
r_mcbond_other1.208
r_angle_other_deg0.854
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.947
r_dihedral_angle_4_deg18.953
r_dihedral_angle_3_deg13.554
r_dihedral_angle_1_deg6.157
r_mcangle_it2.011
r_scbond_it1.757
r_angle_refined_deg1.72
r_mcbond_it1.208
r_mcbond_other1.208
r_angle_other_deg0.854
r_chiral_restr0.093
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
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 Atoms7454
Nucleic Acid Atoms
Solvent Atoms1041
Heterogen Atoms316

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing