8BXT | pdb_00008bxt

Structure of StayGold

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		290	PEG

Crystal Properties
Matthews coefficient	Solvent content
3.07	59.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 133.721	α = 90
b = 133.721	β = 90
c = 58.533	γ = 120

Symmetry
Space Group	P 61

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 EIGER X 16M		2022-07-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04	0.95373	Diamond	I04

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.6	66.66	100	0.062	0.998	9.1	20.5		78841			11.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	100		0.555	0.695	1.6	20.8

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	1.6	66.66	78802	3926	99.928	0.164	0.1633	0.18	0.1846	0.2	15.69

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]
0.367	0.184		0.367		-1.192

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	17.046
r_dihedral_angle_3_deg	13.639
r_dihedral_angle_2_deg	9.024
r_dihedral_angle_1_deg	7.488
r_lrange_it	5.358
r_lrange_other	5.358
r_scangle_it	3.98
r_scangle_other	3.979
r_scbond_it	2.625
r_scbond_other	2.625
r_mcangle_it	2.27
r_mcangle_other	2.27
r_angle_refined_deg	1.52
r_mcbond_it	1.507
r_mcbond_other	1.507
r_angle_other_deg	0.539
r_symmetry_nbd_refined	0.252
r_nbd_refined	0.209
r_symmetry_nbd_other	0.199
r_xyhbond_nbd_refined	0.199
r_nbd_other	0.191
r_nbtor_refined	0.175
r_symmetry_xyhbond_nbd_refined	0.161
r_symmetry_xyhbond_nbd_other	0.111
r_ncsr_local_group_1	0.109
r_symmetry_nbtor_other	0.092
r_chiral_restr	0.079
r_ncsr_local_group_2	0.074
r_gen_planes_refined	0.011
r_bond_refined_d	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3456
Nucleic Acid Atoms
Solvent Atoms	375
Heterogen Atoms	50

Software

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