3HP8 | pdb_00003hp8

Crystal structure of a designed Cyanovirin-N homolog lectin; LKAMG, bound to sucrose

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3HNU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8	277	protein solutions (~40 mg/ml) were incubated overnight with sucrose at a molar ratio of 1:40 (protein:disaccharide) and crystallization were carried out using 0.2 M Li2SO4, 0.1 M Tris-HCl (pH 8.5), and 30% PEG 4000 with protein to mother liquor ratio of 8 to 1 , VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.01	59.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 44.497	α = 90
b = 39.298	β = 97.64
c = 86.134	γ = 90

Symmetry
Space Group	P 1 21 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	IMAGE PLATE	RIGAKU RAXIS IV		2007-05-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT

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	1.88	35.7	96.7	0.166	3.9	3.08		23572		3

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)
	1.88	1.95	76.1		0.413	1.4	2.92

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 (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	3HNU	2	35.7	19030	1022	98.8	0.227	0.224	0.2258	0.277	0.2796	RANDOM	30.47

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]
0.03		-2.26	-1.64		1.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.09
r_dihedral_angle_4_deg	20.972
r_dihedral_angle_3_deg	13.827
r_dihedral_angle_1_deg	6.766
r_scangle_it	4.858
r_scbond_it	3.257
r_mcangle_it	1.873
r_angle_refined_deg	1.596
r_mcbond_it	1.15
r_chiral_restr	0.115
r_bond_refined_d	0.012
r_gen_planes_refined	0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_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	1717
Nucleic Acid Atoms
Solvent Atoms	242
Heterogen Atoms	108

Software

Software
Software Name	Purpose
StructureStudio	data collection
PHASER	phasing
REFMAC	refinement
d*TREK	data reduction
d*TREK	data scaling