7DVB | pdb_00007dvb

D335N variant of Bt4394 in complex with 6SO3-NAG-oxazoline intermediate

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RCN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		282	10 mg/mL protein in the buffer of 25 mM PH 8.0 and 300 mM NaCl was mixed with 0.1 M MES, pH 5.5, 23 % (w/v) PEG 10000 at 1:1 to grow apo crystal. Then the apo was soaked directly with 4MU-6S-GlcNAc powder for 11 min.

Crystal Properties
Matthews coefficient	Solvent content
2.14	42.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.026	α = 90
b = 67.002	β = 94.673
c = 192.803	γ = 90

Symmetry
Space Group	P 1 21 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	PIXEL	DECTRIS PILATUS3 6M		2020-11-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRF BEAMLINE BL18U1	0.979150	SSRF	BL18U1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	2.05	19.716	99.2	0.107	0.998	9.1	6.6		130228

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.05	2.09			1.024	0.53	1.6

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	3rcn	2.05	19.716	130225	6601	99.159	0.23	0.2285	0.23	0.2585	0.26	37.394

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]
-0.66		-0.629	1.133		-0.365

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.925
r_dihedral_angle_4_deg	19.1
r_dihedral_angle_3_deg	14.38
r_dihedral_angle_1_deg	6.422
r_lrange_it	4.577
r_scangle_it	2.901
r_mcangle_it	2.53
r_scbond_it	1.859
r_mcbond_it	1.618
r_angle_refined_deg	0.944
r_nbtor_refined	0.306
r_symmetry_nbd_refined	0.264
r_nbd_refined	0.191
r_symmetry_xyhbond_nbd_refined	0.131
r_xyhbond_nbd_refined	0.122
r_chiral_restr	0.08
r_ncsr_local_group_4	0.071
r_ncsr_local_group_5	0.067
r_ncsr_local_group_2	0.065
r_ncsr_local_group_3	0.063
r_ncsr_local_group_6	0.062
r_ncsr_local_group_1	0.059
r_gen_planes_refined	0.004
r_bond_refined_d	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16687
Nucleic Acid Atoms
Solvent Atoms	454
Heterogen Atoms	91

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction