7BT8 | pdb_00007bt8

Mevo lectin complex with mannotriose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7BSB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICROBATCH	6	296	6%(v/v) Tacsimate pH 6.0, 0.1 M MES monohydrate pH 6.0, 25%(w/v) polyethylene glycol 4000

Crystal Properties
Matthews coefficient	Solvent content
3.36	57.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.77	α = 90
b = 157.22	β = 90
c = 163.18	γ = 90

Symmetry
Space Group	P 2 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV		2018-12-28	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU ULTRAX 18	1.5418

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	2.7	54.39	99	0.19	0.98	7	7		39930

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.7	2.85	100		0.68	1.9

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	THROUGHOUT	7BSB	2.7	54.39	39930	2027	99	0.211	0.2099	0.21	0.2336	0.24	37.967

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]
3.156			-0.532		-2.624

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.264
r_dihedral_angle_4_deg	14.943
r_dihedral_angle_3_deg	14.628
r_lrange_it	9.131
r_lrange_other	9.131
r_dihedral_angle_1_deg	8.437
r_scangle_it	5.882
r_scangle_other	5.882
r_mcangle_it	5.351
r_mcangle_other	5.351
r_scbond_it	3.923
r_scbond_other	3.922
r_mcbond_other	3.426
r_mcbond_it	3.425
r_angle_other_deg	2.427
r_angle_refined_deg	1.663
r_symmetry_nbd_refined	0.298
r_nbd_other	0.271
r_symmetry_nbd_other	0.21
r_symmetry_xyhbond_nbd_refined	0.201
r_nbd_refined	0.178
r_nbtor_refined	0.168
r_xyhbond_nbd_refined	0.133
r_symmetry_xyhbond_nbd_other	0.119
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.064
r_bond_other_d	0.037
r_chiral_restr_other	0.013
r_bond_refined_d	0.01
r_gen_planes_other	0.008
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7220
Nucleic Acid Atoms
Solvent Atoms	61
Heterogen Atoms	162

Software

Software
Software Name	Purpose
REFMAC	refinement
iMOSFLM	data reduction
SCALA	data scaling
PHASER	phasing