9EMY | pdb_00009emy

P. falciparum FIKK13 in complex with ATPgammaS

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	0.2 M LiCl, 20% w/v PEG 6,000, 10% v/v Ethylene Glycol, 0.1M HEPES

Crystal Properties
Matthews coefficient	Solvent content
1.71	27.96

Crystal Data

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

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2023-09-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9537	Diamond	I04

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.81	64.17	99.8	0.196	0.079	0.995	0.212	6.8	7		72257			55.6

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)	Redundancy	Number Unique Reflections (All)
1	2.81	2.86	96.1		2.123	2.286	0.844	0.614	0.4	7.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	2.814	64.169	72156	3699	99.686	0.245	0.2423	0.2423	0.2862	0.2861	74.501

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	-0.963		1.086

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	23.05
r_dihedral_angle_3_deg	16.576
r_dihedral_angle_6_deg	14.689
r_lrange_it	7.863
r_dihedral_angle_1_deg	6.796
r_scangle_it	4.189
r_mcangle_it	3.694
r_scbond_it	2.632
r_mcbond_it	2.219
r_angle_refined_deg	1.549
r_symmetry_nbd_refined	0.32
r_nbtor_refined	0.314
r_symmetry_xyhbond_nbd_refined	0.238
r_nbd_refined	0.235
r_xyhbond_nbd_refined	0.147
r_ncsr_local_group_13	0.132
r_ncsr_local_group_18	0.123
r_ncsr_local_group_8	0.121
r_ncsr_local_group_11	0.119
r_ncsr_local_group_6	0.116
r_ncsr_local_group_14	0.115
r_ncsr_local_group_17	0.109
r_ncsr_local_group_9	0.106
r_chiral_restr	0.099
r_ncsr_local_group_12	0.091
r_ncsr_local_group_10	0.084
r_ncsr_local_group_4	0.082
r_ncsr_local_group_16	0.082
r_ncsr_local_group_1	0.077
r_ncsr_local_group_3	0.077
r_ncsr_local_group_15	0.075
r_ncsr_local_group_2	0.059
r_ncsr_local_group_7	0.049
r_ncsr_local_group_5	0.042
r_gen_planes_refined	0.007
r_bond_refined_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	19014
Nucleic Acid Atoms
Solvent Atoms	18
Heterogen Atoms	148

Software

Software
Software Name	Purpose
REFMAC	refinement
DIALS	data reduction
Aimless	data scaling
PHASER	phasing