6Y2T | pdb_00006y2t

Streptavidin wildtype with a biotC4-1 cofactor - an artificial iron hydroxylase

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	2 M (NH4)2SO4, 0.1 M Na-Acetate, pH 4

Crystal Properties
Matthews coefficient	Solvent content
3	58.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.714	α = 90
b = 57.714	β = 90
c = 184.135	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		2019-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA	1.0000	SLS	X06SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.55	46.076	100	0.069	1	28.8	25.3		23212

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.55	1.58	100		1.704	0.793

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	1.55	46.076	23178	1161	99.931	0.17	0.1688	0.18	0.2004	0.2	23.969

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]
-0.3			-0.3		0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.226
r_dihedral_angle_4_deg	23.562
r_dihedral_angle_3_deg	10.954
r_dihedral_angle_1_deg	7.367
r_lrange_it	6.558
r_lrange_other	6.531
r_scangle_it	4.764
r_scangle_other	4.761
r_scbond_it	3.308
r_scbond_other	3.305
r_mcangle_other	3.254
r_mcangle_it	3.248
r_angle_other_deg	2.514
r_mcbond_it	2.291
r_mcbond_other	2.188
r_angle_refined_deg	2.165
r_symmetry_nbd_refined	0.38
r_nbd_other	0.239
r_symmetry_nbd_other	0.231
r_nbd_refined	0.208
r_nbtor_refined	0.187
r_xyhbond_nbd_refined	0.138
r_symmetry_xyhbond_nbd_refined	0.099
r_chiral_restr	0.084
r_symmetry_nbtor_other	0.084
r_bond_other_d	0.038
r_gen_planes_other	0.023
r_bond_refined_d	0.014
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	904
Nucleic Acid Atoms
Solvent Atoms	101
Heterogen Atoms	100

Software

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