7ZX9 | pdb_00007zx9

Streptavidin with a fluorescent substrate

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	298	2.0 M ammonium sulfate, 0.1 M sodium acetate 26 mg/ml protein

Crystal Properties
Matthews coefficient	Solvent content
2.33	47.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.71	α = 90
b = 57.71	β = 90
c = 183.617	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		2021-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	0.999998	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.546	45.9	95.2	0.092	0.095	0.026	0.999	20.6	20		22167

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.57			2.466	2.643	0.916	0.425		14.9

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	3pk2	1.546	42.024	22140	1091	94.989	0.177	0.176	0.19	0.1993	0.2	29.613

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]
-1.239			-1.239		2.479

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	18.852
r_dihedral_angle_6_deg	16.643
r_dihedral_angle_3_deg	11.916
r_dihedral_angle_1_deg	7.919
r_lrange_it	7.115
r_lrange_other	7.105
r_scangle_other	5.927
r_scangle_it	5.924
r_mcangle_other	4.349
r_mcangle_it	4.347
r_scbond_it	3.957
r_scbond_other	3.954
r_mcbond_it	2.926
r_mcbond_other	2.906
r_angle_refined_deg	1.589
r_angle_other_deg	0.584
r_symmetry_nbd_refined	0.217
r_symmetry_nbd_other	0.2
r_nbd_refined	0.193
r_nbtor_refined	0.182
r_nbd_other	0.171
r_xyhbond_nbd_refined	0.131
r_symmetry_xyhbond_nbd_refined	0.108
r_symmetry_nbtor_other	0.09
r_chiral_restr	0.083
r_chiral_restr_other	0.033
r_bond_refined_d	0.01
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	931
Nucleic Acid Atoms
Solvent Atoms	52
Heterogen Atoms	43

Software

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