6TID | pdb_00006tid

Structure of the N terminal domain of Bc2L-C lectin (1-131) in complex with H-type 1 antigen

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2WQ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	292	1.2 M Na citrate pH 7.0 cryoprotected in 2.5 M sodium malonate

Crystal Properties
Matthews coefficient	Solvent content
1.97	37.45

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.696	α = 90
b = 42.696	β = 90
c = 308.584	γ = 120

Symmetry
Space Group	H 3 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	CCD	ADSC QUANTUM 315		2018-10-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.98096	ESRF	BM30A

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	1.61	36.71	99.7	0.049	0.056	0.027	0.999	23.9	7.8		14606			18.4

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.61	1.64	97.5		0.588	0.643	0.32	0.874	3.7	7.7

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	2wq4	1.614	36.71	14605	751	99.652	0.161	0.1583	0.17	0.2027	0.21	18.654

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]
-0.186	-0.093		-0.186		0.603

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.225
r_dihedral_angle_4_deg	13.944
r_dihedral_angle_3_deg	11.052
r_dihedral_angle_1_deg	8.033
r_lrange_it	5.047
r_lrange_other	4.897
r_scangle_it	3.389
r_scangle_other	3.387
r_mcangle_it	2.526
r_mcangle_other	2.526
r_scbond_it	2.285
r_scbond_other	2.283
r_mcbond_it	1.789
r_mcbond_other	1.782
r_angle_refined_deg	1.779
r_angle_other_deg	1.555
r_nbd_refined	0.208
r_symmetry_nbd_other	0.196
r_symmetry_xyhbond_nbd_refined	0.196
r_nbtor_refined	0.179
r_nbd_other	0.173
r_xyhbond_nbd_refined	0.163
r_symmetry_nbd_refined	0.151
r_chiral_restr	0.099
r_symmetry_nbtor_other	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	967
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	36

Software

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