8VSQ | pdb_00008vsq

Crystal structure of Esub1

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		278	0.2M Lithium sulfate 0.1M Tris pH 8.5 40% PEG 400 12 mg/mL protein

Crystal Properties
Matthews coefficient	Solvent content
3.1	60.28

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.362	α = 90
b = 43.872	β = 118.668
c = 85.841	γ = 90

Symmetry
Space Group	P 1 2 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 PILATUS 6M		2022-11-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	1.1806	CLSI	08ID-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	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	2.9	43.911	99	0.08	0.043	0.999	9.9	3.4		12089

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.9	3.08	94		0.627	0.334	0.94	2

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	2.9	43.911	12087	583	98.46	0.224	0.2217	0.2243	0.2806	0.282

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]
-5.182		-1.009	8.04		-1.098

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.409
r_dihedral_angle_4_deg	17.901
r_dihedral_angle_3_deg	17.377
r_dihedral_angle_1_deg	6.563
r_lrange_it	6.034
r_lrange_other	6.027
r_scangle_it	4.114
r_scangle_other	4.113
r_mcangle_it	3.539
r_mcangle_other	3.537
r_scbond_it	2.466
r_scbond_other	2.465
r_mcbond_it	2.264
r_mcbond_other	2.262
r_angle_refined_deg	1.814
r_angle_other_deg	1.272
r_symmetry_xyhbond_nbd_refined	0.472
r_nbd_other	0.406
r_xyhbond_nbd_other	0.373
r_symmetry_nbd_refined	0.355
r_nbd_refined	0.225
r_symmetry_nbd_other	0.206
r_xyhbond_nbd_refined	0.182
r_nbtor_refined	0.172
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.07
r_ncsr_local_group_1	0.039
r_symmetry_xyhbond_nbd_other	0.021
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3124
Nucleic Acid Atoms
Solvent Atoms	50
Heterogen Atoms	5

Software

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