2WQ8 | pdb_00002wq8

Glycan labelling using engineered variants of galactose oxidase obtained by directed evolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1GOF	PDB ENTRIES 1GOF AND 2EID
experimental model	PDB	2EID	PDB ENTRIES 1GOF AND 2EID

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		5		10% PEG6K, 0.1 M CACL2, 5% GLYCEROL, 10 MM GLCNAC, 50 M ACETATE PH 5.

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 88.464	α = 90
b = 88.464	β = 90
c = 410.846	γ = 120

Symmetry
Space Group	P 65 2 2

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		2008-11-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	2.19	46.6	91.9	0.07	25.34	15.1		43048			29.4

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	2.19	2.23	13.4		0.36	2.43	1.8

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 ENTRIES 1GOF AND 2EID	2.19	76.7	40873	2174	85.33	0.18515	0.18212	0.17	0.24175	0.22	RANDOM	14.489

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]
0.62	0.31		0.62		-0.92

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.442
r_dihedral_angle_4_deg	21.29
r_dihedral_angle_3_deg	15.033
r_dihedral_angle_1_deg	7.402
r_scangle_it	4.785
r_scbond_it	3.302
r_angle_refined_deg	2.113
r_mcangle_it	1.787
r_mcbond_it	1.065
r_chiral_restr	0.148
r_bond_refined_d	0.024
r_gen_planes_refined	0.012
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_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	4826
Nucleic Acid Atoms
Solvent Atoms	382
Heterogen Atoms	64

Software

Software
Software Name	Purpose
HKL-2000	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	phasing
REFMAC	refinement