9SJH | pdb_00009sjh

Crystal structure of apo GHdex dextranase (BT3087), E360A catalytic mutant

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	5AXH

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	2M ammonium sulphate 0.2M Potassium sodium tartrate 0.1M sodium citrate pH 5.6

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.862	α = 90
b = 92.862	β = 90
c = 330.684	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 PILATUS3 6M		2021-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.97940	Diamond	I24

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	2.1	330.68	100	0.892	0.927	0.251	0.99	5.9	25.9		85740

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.14	100		17.905	5.021	0.7	1.2	24.7

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	2.1	89.404	85542	4260	99.931	0.192	0.1903	0.1903	0.2295	0.2295	40.846

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]
1.261			1.261		-2.522

RMS Deviations
Key	Refinement Restraint Deviation
r_lrange_it	26.182
r_dihedral_angle_3_deg	14.058
r_dihedral_angle_6_deg	13.806
r_dihedral_angle_2_deg	13.286
r_scangle_it	7.921
r_dihedral_angle_1_deg	7.124
r_scbond_it	5.528
r_mcangle_it	4.28
r_mcbond_it	3.09
r_angle_refined_deg	1.791
r_symmetry_nbd_refined	0.345
r_nbtor_refined	0.311
r_nbd_refined	0.238
r_xyhbond_nbd_refined	0.206
r_symmetry_xyhbond_nbd_refined	0.151
r_chiral_restr	0.112
r_ncsr_local_group_1	0.064
r_bond_refined_d	0.007
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	9020
Nucleic Acid Atoms
Solvent Atoms	764
Heterogen Atoms	166

Software

Software
Software Name	Purpose
REFMAC	refinement
REFMAC	refinement
Aimless	data scaling
DIALS	data reduction
MrBUMP	phasing
PARROT	phasing
Coot	model building