6UKK | pdb_00006ukk

Crystal Structure of a Domain-swapped Fluorogen Activating Protein DiB3 Dimer

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	3.5	294	0.8 M sodium citrate, 50 mM sodium borate, 0.1 sodium acetate, pH 3.5

Crystal Properties
Matthews coefficient	Solvent content
2.06	40.22

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 89.618	α = 90
b = 38.993	β = 113.21
c = 51.837	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	CCD	MARMOSAIC 300 mm CCD		2018-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	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	1.6	30.94	98.9	0.046	0.021	13.4	4.3		21731			22.124

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.6	1.63	90.2		0.517	0.282	1.8	2.7

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 (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 1QWD	1.6	30.94	20645	1048	98.73	0.1847	0.1839	0.1967	0.1992	0.2104	RANDOM	33.254

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]
2.4		1.78	-1.98		-1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.018
r_dihedral_angle_4_deg	15.033
r_dihedral_angle_3_deg	12.957
r_dihedral_angle_1_deg	7.165
r_mcangle_it	3.709
r_mcbond_it	2.752
r_mcbond_other	2.735
r_angle_other_deg	2.346
r_angle_refined_deg	1.721
r_chiral_restr	0.083
r_bond_other_d	0.035
r_gen_planes_other	0.014
r_bond_refined_d	0.011
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1277
Nucleic Acid Atoms
Solvent Atoms	81
Heterogen Atoms	1

Software

Software
Software Name	Purpose
REFMAC	refinement
MOLREP	phasing
xia2	data scaling
PDB_EXTRACT	data extraction
xia2	data reduction