2FU0

Plasmodium falciparum cyclophilin PFE0505w putative cyclosporin-binding domain


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2B71 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529120% PEG 2000 MME 0.2 M Trimethylamine N-oxide, 0.1 M Tris pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
1.8834.59

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 32.164α = 90
b = 56.301β = 107.89
c = 39.712γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IVVeriMax HR2006-01-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E1.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
11.85098.70.0470.04713.83.2124341243423.8
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8382.60.2340.2342.72.5502

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 (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2B711.837.8124341155286798.70.174370.174370.170830.2211RANDOM23.781
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]
0.46-0.35-0.13-0.54
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.191
r_dihedral_angle_4_deg22.498
r_dihedral_angle_3_deg13.801
r_dihedral_angle_1_deg6.217
r_scangle_it3.056
r_scbond_it1.999
r_mcangle_it1.32
r_angle_refined_deg1.271
r_mcbond_it0.803
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.191
r_dihedral_angle_4_deg22.498
r_dihedral_angle_3_deg13.801
r_dihedral_angle_1_deg6.217
r_scangle_it3.056
r_scbond_it1.999
r_mcangle_it1.32
r_angle_refined_deg1.271
r_mcbond_it0.803
r_nbtor_refined0.309
r_symmetry_vdw_refined0.261
r_nbd_refined0.196
r_xyhbond_nbd_refined0.149
r_symmetry_hbond_refined0.146
r_chiral_restr0.094
r_bond_refined_d0.012
r_gen_planes_refined0.005
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1242
Nucleic Acid Atoms
Solvent Atoms185
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data scaling
PHASERphasing
Cootmodel building
ARP/wARPmodel building