2VUZ

Crystal structure of Codakine in complex with biantennary nonasaccharide at 1.7A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1				0.2M LITHIUM SULFATE IN 100 MM SODIUM ACETATE PH 7.5 WITH 15% PEG 4000

Crystal Properties
Matthews coefficient	Solvent content
2.2	43

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.163	α = 90
b = 100.197	β = 90
c = 95.738	γ = 90

Symmetry
Space Group	C 2 2 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	ADSC CCD	MIRRORS		M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29		ESRF	ID29

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	1.7	34.6	98.6	0.08	5.3	5.6		17204		2	19.7

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	1.7	1.74	99.3		0.38	2	5.7

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2VUV	1.7	50.13	16302	874	98.2	0.204	0.202	0.258	RANDOM	18.48

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]
1.28			0.52		-1.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.288
r_dihedral_angle_3_deg	14.863
r_dihedral_angle_4_deg	10.068
r_dihedral_angle_1_deg	6.997
r_scangle_it	3.25
r_scbond_it	2.306
r_mcangle_it	1.792
r_angle_refined_deg	1.763
r_mcbond_it	1.141
r_angle_other_deg	0.98
r_symmetry_vdw_refined	0.388
r_symmetry_vdw_other	0.254
r_nbd_refined	0.211
r_nbd_other	0.2
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.173
r_symmetry_hbond_refined	0.144
r_chiral_restr	0.103
r_nbtor_other	0.09
r_bond_refined_d	0.018
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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	997
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	109

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing