7EXO | pdb_00007exo

Structure of legume lectin domain from Methanocaldococcus jannaschii in mannose bound form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2BQP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	0.1 M sodium acetate, pH 4.6 and 2 M sodium formate

Crystal Properties
Matthews coefficient	Solvent content
2.52	51.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 55.03	α = 90
b = 55.03	β = 90
c = 149.05	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	IMAGE PLATE	MAR scanner 345 mm plate		2018-12-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	BRUKER AXS MICROSTAR	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.75	51.624	100	0.99	9.4	7.4		24083

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	1.75	1.78			0.743	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	FREE R-VALUE	2BQP	1.75	51.624	24000	1269	99.938	0.161	0.1594	0.17	0.1828	0.2	18.486

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]
0.469			0.469		-0.938

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.437
r_dihedral_angle_3_deg	12.382
r_dihedral_angle_1_deg	8.429
r_lrange_it	6.12
r_lrange_other	6.011
r_scangle_it	4.635
r_scangle_other	4.633
r_scbond_it	2.973
r_scbond_other	2.971
r_mcangle_it	2.428
r_mcangle_other	2.258
r_angle_refined_deg	1.717
r_mcbond_it	1.704
r_angle_other_deg	1.505
r_mcbond_other	1.502
r_dihedral_angle_4_deg	0.423
r_symmetry_nbd_refined	0.24
r_nbd_refined	0.203
r_symmetry_nbd_other	0.2
r_nbd_other	0.185
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.173
r_symmetry_xyhbond_nbd_refined	0.165
r_symmetry_nbtor_other	0.101
r_metal_ion_refined	0.084
r_chiral_restr	0.083
r_bond_refined_d	0.012
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1588
Nucleic Acid Atoms
Solvent Atoms	163
Heterogen Atoms	46

Software

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