6Y34 | pdb_00006y34

Streptavidin wildtype with a biotC5-1 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
2.33	47.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.941	α = 90
b = 57.941	β = 90
c = 183.822	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	1.000	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	1.307	45.998	99.3	0.07	1	26.2	25.4		38242

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	1.307	1.33	95.4		2.702	0.552		22.9

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	1.307	45.998	38091	1873	98.915	0.181	0.1797	0.18	0.1978	0.2	18.282

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]
0.179			0.179		-0.359

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	26.134
r_dihedral_angle_4_deg	25.243
r_dihedral_angle_3_deg	12.093
r_dihedral_angle_1_deg	7.136
r_lrange_it	6.027
r_lrange_other	5.817
r_scangle_it	4.505
r_scangle_other	4.502
r_scbond_it	2.993
r_scbond_other	2.99
r_angle_other_deg	2.69
r_mcangle_it	2.637
r_mcangle_other	2.636
r_angle_refined_deg	2.235
r_mcbond_it	1.807
r_mcbond_other	1.777
r_chiral_restr	0.309
r_symmetry_nbd_other	0.232
r_nbd_other	0.198
r_nbd_refined	0.194
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.177
r_xyhbond_nbd_refined	0.141
r_symmetry_nbtor_other	0.087
r_symmetry_xyhbond_nbd_refined	0.076
r_bond_other_d	0.038
r_gen_planes_other	0.02
r_bond_refined_d	0.017
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	904
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	23

Software

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