4QT2

Crystal Structure of the FK506-Binding Domain of Plasmodium Falciparum FKBP35 in complex with Rapamycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2VN1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72910.1M MIB, 25% PEG1500, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.7329.02

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.812α = 90
b = 48.7β = 90
c = 58.933γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2014-05-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-20.8726ESRFID23-2

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.4437.5497.81937026.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2VN11.4437.54193701893094097.770.15310.14980.2156RANDOM16.654
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]
-0.760.76
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.68
r_sphericity_free25.273
r_dihedral_angle_4_deg15.409
r_dihedral_angle_3_deg14.164
r_dihedral_angle_1_deg6.56
r_sphericity_bonded6.536
r_rigid_bond_restr6.426
r_mcangle_it2.076
r_angle_refined_deg1.813
r_mcbond_it1.766
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.68
r_sphericity_free25.273
r_dihedral_angle_4_deg15.409
r_dihedral_angle_3_deg14.164
r_dihedral_angle_1_deg6.56
r_sphericity_bonded6.536
r_rigid_bond_restr6.426
r_mcangle_it2.076
r_angle_refined_deg1.813
r_mcbond_it1.766
r_mcbond_other1.755
r_angle_other_deg1.493
r_chiral_restr0.712
r_bond_refined_d0.012
r_gen_planes_refined0.005
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms959
Nucleic Acid Atoms
Solvent Atoms99
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
DNAdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing