3T6L | pdb_00003t6l

Y54F mutant of core streptavidin

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MM9	PDB ENTRY 1MM9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.2	293	2.5 M sodium chloride, 0.1 M sodium-potassium phosphate (30% ethylene glycol cryoprotectant), pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.65	53.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.273	α = 90
b = 57.273	β = 90
c = 171.715	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	PSI PILATUS 6M		2011-01-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL12-2	1.0	SSRL	BL12-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.15	36.628	99.1	0.057	21.8	14.7	35684	35679

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.15	1.21	93.6		0.967	2.3	9.6	6957

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1MM9	1.3	36.628	33868	33868	1811	99.97	0.1366	0.1366	0.1353	0.14	0.16	0.16	RANDOM	17.4686

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		-0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.349
r_dihedral_angle_4_deg	13.099
r_dihedral_angle_3_deg	10.838
r_sphericity_free	10.679
r_dihedral_angle_1_deg	7.547
r_scangle_it	6.05
r_sphericity_bonded	5.305
r_scbond_it	4.565
r_mcangle_it	4.293
r_mcbond_it	3.11
r_mcbond_other	2.469
r_rigid_bond_restr	2.217
r_angle_refined_deg	1.826
r_angle_other_deg	1.027
r_chiral_restr	0.126
r_bond_refined_d	0.017
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	897
Nucleic Acid Atoms
Solvent Atoms	112
Heterogen Atoms	5

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection
XDS	data reduction
XDS	data scaling
BALBES	phasing