2ZQO | pdb_00002zqo

Crystal structure of the earthworm R-type lectin C-half in complex with GalNAc

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1XYF	PDB ENTRY 1XYF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8	293	sodium chloride, dipotassium hydrogen phosphate, sodium dihydrogen phosphate, imidazole, cadmium chloride, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.21	α = 90
b = 34.747	β = 104.2
c = 61.586	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	95	CCD	ADSC QUANTUM 4		2004-11-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-6A	1.0	Photon Factory	BL-6A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.8	50	94	0.098	36.1	7.2		23141

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.8	1.86	94		0.308	8.6	7	2213

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1XYF	1.8	48.62	23837	21951	1190	97.08	0.19542	0.19212	0.1921	0.25981	0.2594	RANDOM	15.126

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.132
r_dihedral_angle_4_deg	17.329
r_dihedral_angle_3_deg	14.569
r_dihedral_angle_1_deg	6.326
r_scangle_it	3.306
r_scbond_it	2.199
r_mcangle_it	1.437
r_angle_refined_deg	1.423
r_mcbond_it	0.882
r_nbtor_refined	0.306
r_symmetry_hbond_refined	0.252
r_symmetry_vdw_refined	0.223
r_nbd_refined	0.193
r_xyhbond_nbd_refined	0.151
r_chiral_restr	0.095
r_bond_refined_d	0.014
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2077
Nucleic Acid Atoms
Solvent Atoms	315
Heterogen Atoms	81

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing