4CP9 | pdb_00004cp9

Crystal structure OF lecA lectin complexed with a divalent galactoside at 1.65 angstrom

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.5		SOLUTION 20 OF THE CSSI SCREEN 8% PEG 20K, 8% PEG550MME, 100 MM TRIS 8.5 AND 0.2 M LI2SO4

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.3

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 50.876	α = 90
b = 66.259	β = 90
c = 159.427	γ = 90

Symmetry
Space Group	P 21 21 21

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	MARRESERACH		2013-07-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2		ESRF	ID23-2

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	1.65	48.47	100	0.04	22.9	5.4		65807		2

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	1.65	1.68	100		0.51	3	5.5

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 (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 1OKO	1.65	48.47	62390	3334	99.91	0.15665	0.15525	0.17	0.18362	0.19	RANDOM	26.643

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]
-0.75			2.17		-1.42

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.637
r_dihedral_angle_3_deg	10.707
r_dihedral_angle_1_deg	6.041
r_dihedral_angle_4_deg	5.514
r_scbond_it	2.17
r_mcangle_it	1.809
r_angle_refined_deg	1.725
r_mcbond_it	1.201
r_mcbond_other	1.2
r_angle_other_deg	0.783
r_symmetry_vdw_refined	0.28
r_nbd_refined	0.241
r_nbd_other	0.181
r_nbtor_refined	0.178
r_symmetry_vdw_other	0.178
r_metal_ion_refined	0.154
r_symmetry_hbond_refined	0.133
r_xyhbond_nbd_refined	0.106
r_chiral_restr	0.105
r_nbtor_other	0.081
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3614
Nucleic Acid Atoms
Solvent Atoms	418
Heterogen Atoms	194

Software

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