9FGP | pdb_00009fgp

cilia and flagella associated protein 299

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold	Q6V702

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6	293	20% PEG6000 -- 10% ethylene glycol -- 0.1M MES pH 6.0 -- 0.01M zinc chloride

Crystal Properties
Matthews coefficient	Solvent content
1.96	37.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 31.756	α = 91.354
b = 34.449	β = 100.003
c = 58.984	γ = 90.09

Symmetry
Space Group	P 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 EIGER2 XE 16M		2022-08-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.49	58.071	71.6	0.998	1.29	3.5		28810			8.45

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.49	1.52			0.925

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	1.49	58.071	28809	1450	71.625	0.177	0.1745	0.17	0.2189	0.22	13.565

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]
-0.357	0.219	-0.03	-0.22	0.395	0.534

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.583
r_dihedral_angle_3_deg	13.235
r_dihedral_angle_1_deg	7.4
r_dihedral_angle_2_deg	6.775
r_lrange_it	5.058
r_scangle_it	3.179
r_mcangle_it	2.186
r_scbond_it	2.113
r_angle_refined_deg	1.962
r_mcbond_it	1.361
r_nbtor_refined	0.317
r_nbd_refined	0.212
r_symmetry_nbd_refined	0.183
r_symmetry_xyhbond_nbd_refined	0.182
r_xyhbond_nbd_refined	0.156
r_chiral_restr	0.131
r_symmetry_metal_ion_refined	0.091
r_ncsr_local_group_1	0.074
r_metal_ion_refined	0.061
r_bond_refined_d	0.01
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2279
Nucleic Acid Atoms
Solvent Atoms	264
Heterogen Atoms	12

Software

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