4MGV

Crystal structure of FK506 binding domain of plasmodium VIVAX FKBP35 In complex with inhibitor D5


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3IHZ 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP92913.0M AMMONIUM SULPHATE, 0.1M BICINE, pH 9.0, 30mM Glycl-Glycl-Glycine, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.0740.65

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 51.45α = 90
b = 46.01β = 117.37
c = 55.1γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++MIRRORS2011-11-10MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.5418

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
11.7233.52990.03418.33.512119
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)
11.721.8194.10.16252.91662

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 REPLACEMENTTHROUGHOUT3IHZ1.722011028107098.860.203180.199970.23529RANDOM30.681
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]
-0.440.451.68-0.83
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.64
r_dihedral_angle_4_deg22.237
r_dihedral_angle_3_deg13.896
r_dihedral_angle_1_deg6.587
r_scangle_it4.09
r_scbond_it2.546
r_mcangle_it1.768
r_angle_refined_deg1.557
r_mcbond_it0.975
r_chiral_restr0.095
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.64
r_dihedral_angle_4_deg22.237
r_dihedral_angle_3_deg13.896
r_dihedral_angle_1_deg6.587
r_scangle_it4.09
r_scbond_it2.546
r_mcangle_it1.768
r_angle_refined_deg1.557
r_mcbond_it0.975
r_chiral_restr0.095
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms943
Nucleic Acid Atoms
Solvent Atoms126
Heterogen Atoms22

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling