9SJG | pdb_00009sjg

Crystal structure of apo GHdex dextranase (BT3087), wild type

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		Used our previously solved BT3087 E360A structure to solve phases

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		293	0.1M MES 0.8-3.2M ammonium sulphate

Crystal Properties
Matthews coefficient	Solvent content
2.8	56.02

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 93.698	α = 90
b = 93.698	β = 90
c = 331.612	γ = 90

Symmetry
Space Group	P 41 21 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		2021-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.89842	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	1.8	55.27	100	0.161	0.167	0.046	0.999	13.4	25.1		137723

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)
	1.8	1.83	100		2.239	2.323	0.618	0.81	1.6	27.3

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	1.8	54.133	137436	6909	99.9	0.2	0.1982	0.1982	0.2291	0.2291	31.862

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]
0.952			0.952		-1.905

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	23.018
r_dihedral_angle_2_deg	17.941
r_dihedral_angle_6_deg	15.325
r_dihedral_angle_3_deg	11.967
r_dihedral_angle_1_deg	7.015
r_scangle_it	6.074
r_scbond_it	4.303
r_mcangle_it	3.29
r_mcbond_it	2.627
r_angle_refined_deg	1.815
r_metal_ion_refined	0.589
r_nbtor_refined	0.312
r_symmetry_nbd_refined	0.284
r_nbd_refined	0.232
r_xyhbond_nbd_refined	0.198
r_symmetry_xyhbond_nbd_refined	0.185
r_chiral_restr	0.132
r_ncsr_local_group_1	0.066
r_bond_refined_d	0.009
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9008
Nucleic Acid Atoms
Solvent Atoms	1418
Heterogen Atoms	131

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
DIALS	data collection
Coot	model building
PHASER	phasing