8AQD | pdb_00008aqd

Hydrophobic probe bound to Streptavidin - 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3PK2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4	293	25 w/v% PEG 3350 0.1 M sodium acetate pH 4.0

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.581	α = 90
b = 57.581	β = 90
c = 183.943	γ = 90

Symmetry
Space Group	I 41 2 2

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		2022-07-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0000413700316724	SLS	X06SA

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	1.45	46.03	100	0.997	15.4	20		28050

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	1.45	1.47			0.812

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 (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3pk2	1.45	46.03	26587	1433	99.94	0.187	0.1842	0.1881	0.2396	0.2423	RANDOM	21.121

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]
0.27			0.27		-0.54

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	12.409
r_dihedral_angle_2_deg	9.038
r_dihedral_angle_1_deg	7.687
r_rigid_bond_restr	5.629
r_angle_refined_deg	1.502
r_angle_other_deg	0.558
r_chiral_restr	0.076
r_gen_planes_refined	0.011
r_bond_refined_d	0.009
r_bond_other_d	0.003
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	928
Nucleic Acid Atoms
Solvent Atoms	107
Heterogen Atoms	72

Software

Software
Software Name	Purpose
Aimless	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
PHASER	phasing