9EMY | pdb_00009emy

P. falciparum FIKK13 in complex with ATPgammaS


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelAlphaFold 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP72980.2 M LiCl, 20% w/v PEG 6,000, 10% v/v Ethylene Glycol, 0.1M HEPES
Crystal Properties
Matthews coefficientSolvent content
1.7127.96

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.397α = 90
b = 121.657β = 90.02
c = 151.059γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2023-09-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9537DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)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
12.8164.1799.80.1960.0790.9950.2126.877225755.6
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.812.8696.12.1232.2860.8440.6140.47.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.81464.16972156369999.6860.2450.24230.24230.28620.286174.501
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]
-0.124-0.015-0.9631.086
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.05
r_dihedral_angle_3_deg16.576
r_dihedral_angle_6_deg14.689
r_lrange_it7.863
r_dihedral_angle_1_deg6.796
r_scangle_it4.189
r_mcangle_it3.694
r_scbond_it2.632
r_mcbond_it2.219
r_angle_refined_deg1.549
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg23.05
r_dihedral_angle_3_deg16.576
r_dihedral_angle_6_deg14.689
r_lrange_it7.863
r_dihedral_angle_1_deg6.796
r_scangle_it4.189
r_mcangle_it3.694
r_scbond_it2.632
r_mcbond_it2.219
r_angle_refined_deg1.549
r_symmetry_nbd_refined0.32
r_nbtor_refined0.314
r_symmetry_xyhbond_nbd_refined0.238
r_nbd_refined0.235
r_xyhbond_nbd_refined0.147
r_ncsr_local_group_130.132
r_ncsr_local_group_180.123
r_ncsr_local_group_80.121
r_ncsr_local_group_110.119
r_ncsr_local_group_60.116
r_ncsr_local_group_140.115
r_ncsr_local_group_170.109
r_ncsr_local_group_90.106
r_chiral_restr0.099
r_ncsr_local_group_120.091
r_ncsr_local_group_100.084
r_ncsr_local_group_40.082
r_ncsr_local_group_160.082
r_ncsr_local_group_10.077
r_ncsr_local_group_30.077
r_ncsr_local_group_150.075
r_ncsr_local_group_20.059
r_ncsr_local_group_70.049
r_ncsr_local_group_50.042
r_gen_planes_refined0.007
r_bond_refined_d0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms19014
Nucleic Acid Atoms
Solvent Atoms18
Heterogen Atoms148

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
PHASERphasing