9SJJ | pdb_00009sjj

Crystal structure of SusDdex (BT3089) with bound IMO5

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	6GCZ	Used previously solved BT3089 structure for MR, which was originally solved by PDB 6GCZ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.5	293	0.2M Lithium sulfate 0.1M Sodium acetate pH 4.5 50% w/v PEG 400 Soaked ~10 mM dextran 1.5 into grown crystals (1 crystal per drop), which cracked the large crystal. This was one fragment harvested for the synchrotron.

Crystal Properties
Matthews coefficient	Solvent content
2.97	58.55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 87	α = 90
b = 106.15	β = 90
c = 138.34	γ = 90

Symmetry
Space Group	I 2 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 EIGER2 XE 16M		2021-05-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97960	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim 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	1.7	67.29	100	0.096	0.1	0.028	1	19.4	25.3		70548

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.7	1.73	100		3.015	3.129	0.832	0.587	1.3	27.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.7	67.288	70548	3544	99.991	0.166	0.1647	0.1647	0.191	0.1909	35.229

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]
-1.001			0.457		0.545

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	15.3
r_dihedral_angle_3_deg	12.773
r_lrange_it	7.354
r_dihedral_angle_2_deg	7.255
r_scangle_it	6.437
r_dihedral_angle_1_deg	6.396
r_scbond_it	4.788
r_mcangle_it	3.876
r_mcbond_it	2.91
r_angle_refined_deg	2.075
r_nbtor_refined	0.318
r_nbd_refined	0.21
r_symmetry_nbd_refined	0.183
r_chiral_restr	0.141
r_xyhbond_nbd_refined	0.12
r_symmetry_xyhbond_nbd_refined	0.064
r_bond_refined_d	0.014
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3645
Nucleic Acid Atoms
Solvent Atoms	310
Heterogen Atoms	224

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
MOLREP	phasing
Coot	model building
BUSTER	refinement
PHASER	phasing
BUCCANEER	model building