7BT9 | pdb_00007bt9

Mevo lectin complex with alpha-mannose

X-RAY DIFFRACTION

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Starting Model(s)

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

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
2.82	56.36

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 168.849	α = 90
b = 168.849	β = 90
c = 193.639	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		2019-09-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ELETTRA BEAMLINE 11.2C	0.979	ELETTRA	11.2C

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	2.45	96.82	98.4	0.22	0.99	6.1	10.7		101188

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	2.45	2.58			0.75	1.5

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	7BSM	2.45	84.567	100875	5072	98.115	0.244	0.2423	0.25	0.2837	0.28	36.231

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]
-4.301			-4.301		8.602

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.081
r_dihedral_angle_3_deg	16.34
r_dihedral_angle_4_deg	12.923
r_lrange_other	8.957
r_lrange_it	8.956
r_dihedral_angle_1_deg	8.467
r_scangle_it	5.691
r_scangle_other	5.691
r_mcangle_it	5.286
r_mcangle_other	5.286
r_scbond_it	3.702
r_scbond_other	3.702
r_mcbond_it	3.413
r_mcbond_other	3.413
r_angle_other_deg	2.477
r_angle_refined_deg	1.891
r_nbd_other	0.279
r_symmetry_nbd_other	0.22
r_symmetry_xyhbond_nbd_refined	0.188
r_nbd_refined	0.183
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.156
r_symmetry_nbd_refined	0.12
r_symmetry_nbtor_other	0.081
r_chiral_restr	0.073
r_symmetry_xyhbond_nbd_other	0.058
r_bond_other_d	0.037
r_bond_refined_d	0.012
r_gen_planes_other	0.009
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	14576
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	168

Software

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