6Y2M | pdb_00006y2m

Streptavidin mutant S112R 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
2.24	45.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.146	α = 90
b = 57.146	β = 90
c = 182.564	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	1.95	45.69	100	0.102	0.999	23.2	24.1		11549

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	1.95	2	100		1.9	0.907		26

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	1.95	45.64	11469	576	99.419	0.193	0.1914	0.2	0.2305	0.24	37.149

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]
0.39			0.39		-0.781

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.069
r_dihedral_angle_4_deg	23.088
r_dihedral_angle_3_deg	13.913
r_dihedral_angle_1_deg	8.286
r_lrange_other	7.343
r_lrange_it	7.299
r_scangle_other	5.624
r_scangle_it	5.513
r_mcangle_it	4.345
r_mcangle_other	4.342
r_scbond_other	3.944
r_scbond_it	3.912
r_mcbond_it	3.33
r_mcbond_other	3.328
r_angle_other_deg	2.548
r_angle_refined_deg	1.858
r_nbd_other	0.264
r_symmetry_nbd_other	0.232
r_nbd_refined	0.216
r_symmetry_nbd_refined	0.197
r_symmetry_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.123
r_symmetry_nbtor_other	0.082
r_chiral_restr	0.075
r_bond_other_d	0.038
r_gen_planes_other	0.015
r_bond_refined_d	0.012
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	923
Nucleic Acid Atoms
Solvent Atoms	58
Heterogen Atoms	44

Software

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