7YIA | pdb_00007yia

Crystal structure of K74A mutant of Cap4 SAVED domain-containing receptor from Enterobacter cloacae

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7YIB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	0.1 M Bis-Tris propane pH 6.5, 0.2 M sodium acetate, 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.68	54.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.901	α = 90
b = 70.212	β = 90
c = 150.734	γ = 90

Symmetry
Space Group	P 2 21 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	CCD	RAYONIX MX300-HS		2021-10-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSRRC BEAMLINE TPS 05A	0.99984	NSRRC	TPS 05A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.42	30	98.1	0.06	28.7	6.9		23087

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.42	2.51	99.5		0.653	2.1	5.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	7YIB	2.428	29.895	20808	1033	88.308	0.203	0.2019	0.21	0.2192	0.22	41.116

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]
0.639			-0.602		-0.037

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.785
r_dihedral_angle_4_deg	18.476
r_dihedral_angle_3_deg	15.647
r_lrange_other	9.14
r_lrange_it	9.137
r_dihedral_angle_1_deg	8.298
r_mcangle_it	6.403
r_mcangle_other	6.401
r_scangle_it	6.366
r_scangle_other	6.366
r_mcbond_other	4.102
r_mcbond_it	4.101
r_scbond_it	4.072
r_scbond_other	4.071
r_angle_refined_deg	1.414
r_angle_other_deg	1.226
r_nbd_other	0.255
r_nbd_refined	0.205
r_symmetry_nbd_other	0.202
r_symmetry_nbd_refined	0.168
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.135
r_symmetry_xyhbond_nbd_refined	0.12
r_symmetry_nbtor_other	0.078
r_chiral_restr	0.06
r_symmetry_xyhbond_nbd_other	0.051
r_bond_refined_d	0.01
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3915
Nucleic Acid Atoms
Solvent Atoms	135
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing