7XSG | pdb_00007xsg

Crystal structure of ClAgl29B

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	AlphaFold		AlphaFold2 model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	293	0.1 M sodium citrate (pH 3.5), 5% PEG 20,000, 5% 2-propanol

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.132	α = 90
b = 123.405	β = 90
c = 166.605	γ = 90

Symmetry
Space Group	P 21 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	PIXEL	DECTRIS PILATUS 2M		2021-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0	Photon Factory	AR-NE3A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rrim 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	1.609	99.165	99.5	0.063	0.069	0.999	22.17	6.7		194275			22.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.61	1.71	97		0.423	0.459	0.942	4.51	6.6

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	FREE R-VALUE	AlphaFold2 model	1.609	45.418	194274	9719	99.483	0.173	0.1722	0.18	0.1884	0.2	18.001

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]
1.04			-0.245		-0.795

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	16.334
r_dihedral_angle_3_deg	13.835
r_dihedral_angle_2_deg	9.784
r_dihedral_angle_1_deg	6.649
r_lrange_it	4.961
r_lrange_other	4.734
r_scangle_it	3.488
r_scangle_other	3.488
r_mcangle_it	2.496
r_mcangle_other	2.496
r_scbond_it	2.275
r_scbond_other	2.275
r_mcbond_it	1.665
r_mcbond_other	1.663
r_angle_refined_deg	1.364
r_angle_other_deg	0.472
r_symmetry_nbd_refined	0.275
r_nbd_refined	0.223
r_nbd_other	0.207
r_symmetry_xyhbond_nbd_refined	0.205
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.126
r_metal_ion_refined	0.107
r_ncsr_local_group_1	0.086
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.07
r_gen_planes_refined	0.008
r_bond_refined_d	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8828
Nucleic Acid Atoms
Solvent Atoms	1008
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHENIX	phasing