8S1Y | pdb_00008s1y

ThaOS V79A

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293.15	(30 mM sodium nitrate, 30 mM sodium phosphate, 30 mM ammonium sulfate, 100 mM HEPES/MOPS pH 7.5, 12.5% (w/v) PEG1000 and 12.5% (w/v) PEG3350), P21 (30 mM magnesium chloride, 30 mM calcium chloride, 100 mM HEPES/MOPS pH 7.5, 12.5% (w/v) PEG1000 and 12.5% (w/v) PEG3350)

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.43	α = 64.8
b = 63.94	β = 70.29
c = 65.97	γ = 68.18

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 PILATUS 6M		2021-07-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.9794	Diamond	I04

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	1.5	43.76	96.1	1	15.3	3.5		118545

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	1.5	1.53			0.521		3.5

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	1.5	43.758	118545	5892	96.063	0.161	0.159	0.159	0.192	0.192	24.931

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]
-0.443	0.145	0.201	0.231	0.005	0.236

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.324
r_dihedral_angle_3_deg	14.48
r_dihedral_angle_2_deg	9.686
r_lrange_it	6.664
r_lrange_other	6.664
r_dihedral_angle_1_deg	6.251
r_scangle_it	6.077
r_scangle_other	6.076
r_scbond_it	4.353
r_scbond_other	4.353
r_mcangle_it	3.087
r_mcangle_other	3.087
r_mcbond_it	2.471
r_mcbond_other	2.471
r_angle_refined_deg	2.069
r_angle_other_deg	0.656
r_symmetry_nbd_refined	0.254
r_nbd_other	0.231
r_nbd_refined	0.222
r_symmetry_nbd_other	0.19
r_nbtor_refined	0.184
r_xyhbond_nbd_refined	0.152
r_symmetry_xyhbond_nbd_refined	0.152
r_chiral_restr	0.113
r_ncsr_local_group_1	0.091
r_symmetry_nbtor_other	0.085
r_xyhbond_nbd_other	0.028
r_symmetry_xyhbond_nbd_other	0.023
r_chiral_restr_other	0.018
r_bond_refined_d	0.015
r_gen_planes_refined	0.012
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6137
Nucleic Acid Atoms
Solvent Atoms	555
Heterogen Atoms	96

Software

Software
Software Name	Purpose
REFMAC	refinement
Aimless	data scaling
xia2	data reduction
XDS	data reduction
PHASER	phasing
MolProbity	model building
Coot	model building