2BFP

Leishmania major pteridine reductase 1 in complex with NADP and tetrahydrobiopterin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1E92PDB ENTRY 1E92

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.529315 MG/ML PROTEIN, 0.1M NAAC/HAC BUFFER PH 5.5, 13% MPEG 5000, 0.07M CAAC2, 293K
Crystal Properties
Matthews coefficientSolvent content
2.754

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 94.103α = 90
b = 103.566β = 90
c = 137.434γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
12.552598.20.0817.24.84362451.1
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)
12.552.65980.265.6

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 1E922.5524.54125921851000.20.1980.238RANDOM46.61
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]
0.25-0.07-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.341
r_scbond_it2.685
r_dihedral_angle_1_deg2.595
r_mcangle_it1.823
r_angle_refined_deg1.531
r_mcbond_it0.876
r_symmetry_hbond_refined0.299
r_nbd_refined0.218
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.115
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.341
r_scbond_it2.685
r_dihedral_angle_1_deg2.595
r_mcangle_it1.823
r_angle_refined_deg1.531
r_mcbond_it0.876
r_symmetry_hbond_refined0.299
r_nbd_refined0.218
r_symmetry_vdw_refined0.18
r_xyhbond_nbd_refined0.115
r_chiral_restr0.112
r_bond_refined_d0.008
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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 Atoms7791
Nucleic Acid Atoms
Solvent Atoms152
Heterogen Atoms284

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing