2V6T

Crystal structure of a complex of pterin-4a-carbinolamine dehydratase from Toxoplasma gondii with 7,8-dihydrobiopterin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2V6SPDB ENTRY 2V6S

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.60.4 M POTASSIUM-SODIUM TARTRATE, pH 7.6
Crystal Properties
Matthews coefficientSolvent content
3.8267.6

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 119.51α = 90
b = 119.51β = 90
c = 49.928γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEOSMIC CONFOCAL OPTICS2006-12-07MSINGLE 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
13.1431000.0511.59.269693
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)
13.13.271000.471.69.4

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 2V6S3.142.99659134199.90.190.1870.271RANDOM79.11
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]
0.090.09-0.18
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.77
r_dihedral_angle_3_deg22.207
r_dihedral_angle_4_deg21.6
r_dihedral_angle_1_deg11.436
r_scangle_it3.617
r_scbond_it2.283
r_angle_refined_deg2.254
r_mcangle_it1.592
r_mcbond_it0.811
r_nbtor_refined0.326
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.77
r_dihedral_angle_3_deg22.207
r_dihedral_angle_4_deg21.6
r_dihedral_angle_1_deg11.436
r_scangle_it3.617
r_scbond_it2.283
r_angle_refined_deg2.254
r_mcangle_it1.592
r_mcbond_it0.811
r_nbtor_refined0.326
r_nbd_refined0.286
r_symmetry_hbond_refined0.259
r_symmetry_vdw_refined0.237
r_xyhbond_nbd_refined0.149
r_chiral_restr0.143
r_bond_refined_d0.022
r_gen_planes_refined0.008
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 Atoms1622
Nucleic Acid Atoms
Solvent Atoms11
Heterogen Atoms34

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing