6VJL | pdb_00006vjl

Streptavidin mutant M112 (G26C/A46C)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1SWE

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	294.15	28% PEG 4000, 0.15 M ammonium sulfate, 50 mM Bis-Tris

Crystal Properties
Matthews coefficient	Solvent content
2.3	46.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.772	α = 90
b = 57.772	β = 90
c = 184.419	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 PILATUS3 S 6M		2017-04-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim 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	1.3	50	99.9	0.073	0.073	0.076	1	19.6	11		39166

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.3	1.33	99.2		0.0101	0.0101	1.11	0.577		5.6

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	THROUGHOUT	1SWE	1.3	37.35	38946	2002	99.872	0.191	0.19	0.1974	0.2009	0.2071	19.813

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]
0.231			0.231		-0.462

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	25.805
r_dihedral_angle_3_deg	10.932
r_dihedral_angle_4_deg	10.378
r_lrange_it	7.333
r_dihedral_angle_1_deg	6.593
r_scangle_it	4.168
r_mcangle_it	2.92
r_scbond_it	2.762
r_mcbond_it	1.911
r_angle_refined_deg	1.336
r_nbtor_refined	0.284
r_symmetry_nbd_refined	0.151
r_nbd_refined	0.15
r_chiral_restr	0.083
r_symmetry_xyhbond_nbd_refined	0.072
r_xyhbond_nbd_refined	0.061
r_bond_refined_d	0.007
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	918
Nucleic Acid Atoms
Solvent Atoms	156
Heterogen Atoms	16

Software

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