1WMY | pdb_00001wmy

Crystal Structure of C-type Lectin CEL-I from Cucumaria echinata

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1LIT	PDB Entry 1LIT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	60% 2-methyl-2,4-pentanediol, 10mM calcium chloride, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.64	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 92.38	α = 90
b = 69.94	β = 136.46
c = 76.69	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	100	CCD	ADSC QUANTUM 4		2001-02-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE BL-18B	1.00	Photon Factory	BL-18B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2	52.7	92.3			20936	20936			12.6

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	82.2

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 (All)	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 1LIT	2	52.7	19924	19924	1012		0.14016	0.14016	0.13813	0.15	0.1792	0.19	RANDOM	25.338

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]
-1.2		-1.59	-0.18		-0.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.159
r_scangle_it	4.506
r_scbond_it	3.073
r_mcangle_it	1.804
r_angle_refined_deg	1.702
r_mcbond_it	1.15
r_angle_other_deg	0.904
r_symmetry_vdw_other	0.301
r_nbd_other	0.264
r_nbd_refined	0.225
r_symmetry_hbond_refined	0.225
r_symmetry_vdw_refined	0.194
r_xyhbond_nbd_refined	0.161
r_chiral_restr	0.116
r_nbtor_other	0.09
r_metal_ion_refined	0.086
r_bond_refined_d	0.022
r_gen_planes_refined	0.01
r_gen_planes_other	0.007
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2268
Nucleic Acid Atoms
Solvent Atoms	247
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
DPS	data reduction
CCP4	data scaling
AMoRE	phasing