9QVB | pdb_00009qvb

Structure of Eimeria tenella SAG13 (ETH_00013178)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6ZZB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.9	290	0.2 M potassium nitrate pH6.9, 20% w/v PEG3350

Crystal Properties
Matthews coefficient	Solvent content
2.32	47.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.57	α = 90
b = 65.16	β = 90
c = 114.6	γ = 90

Symmetry
Space Group	C 2 2 21

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		2023-03-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97623	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	1.7	39.5	100	0.23	0.997	0.9969	7.55	13.25		20477

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.7	1.74	100		2.94	0.3	0.3012	0.82

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	FREE R-VALUE	1.75	39.483	19145	956	99.99	0.19	0.1875	0.196	0.2451	0.2503	23.384

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]
-0.007			-0.253		0.26

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.309
r_dihedral_angle_3_deg	11.688
r_dihedral_angle_2_deg	8.096
r_dihedral_angle_1_deg	6.686
r_lrange_it	5.28
r_lrange_other	5.228
r_scangle_it	4.199
r_scangle_other	4.196
r_scbond_it	2.774
r_scbond_other	2.773
r_mcangle_other	2.46
r_mcangle_it	2.457
r_angle_refined_deg	1.989
r_mcbond_it	1.802
r_mcbond_other	1.802
r_angle_other_deg	0.657
r_nbd_refined	0.232
r_nbd_other	0.209
r_symmetry_nbd_refined	0.202
r_symmetry_nbd_other	0.189
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.093
r_symmetry_xyhbond_nbd_refined	0.093
r_symmetry_nbtor_other	0.083
r_bond_refined_d	0.011
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1351
Nucleic Acid Atoms
Solvent Atoms	154
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing