6TLB

Plasmodium falciparum lipocalin (PF3D7_0925900)


X-RAY DIFFRACTION - SOLUTION SCATTERING

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION72920.2 M magnesium chloride, 0.1 M Tris pH7, 2.5 M Sodium Chloride
Crystal Properties
Matthews coefficientSolvent content
3.766.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 63.993α = 90
b = 92.25β = 98.35
c = 214.502γ = 90
Symmetry
Space GroupI 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2019-03-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)0.9762PETRA III, EMBL c/o DESYP13 (MX1)

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)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
12.8556.299.750.19850.29430.5463.6922893654.95
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)R Split (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.852.9520.411.19

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Cut-off Sigma (I)Cut-off Sigma (F)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 REPLACEMENT2.8556.227535142899.750.19120.188860.23647RANDOM53.494
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]
-0.09-0.040.090.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.265
r_dihedral_angle_4_deg19.276
r_dihedral_angle_3_deg17.812
r_long_range_B_other11.251
r_long_range_B_refined11.234
r_dihedral_angle_1_deg9.775
r_scangle_other7.468
r_mcangle_other6.898
r_mcangle_it6.895
r_scbond_it4.654
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg41.265
r_dihedral_angle_4_deg19.276
r_dihedral_angle_3_deg17.812
r_long_range_B_other11.251
r_long_range_B_refined11.234
r_dihedral_angle_1_deg9.775
r_scangle_other7.468
r_mcangle_other6.898
r_mcangle_it6.895
r_scbond_it4.654
r_scbond_other4.604
r_mcbond_it4.33
r_mcbond_other4.313
r_angle_refined_deg1.539
r_angle_other_deg1.208
r_chiral_restr0.064
r_bond_refined_d0.007
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5930
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms27

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing