2DTS

Crystal Structure of the Defucosylated Fc Fragment from Human Immunoglobulin G1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1H3X	PDB ENTRY 1H3X

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	MICRODIALYSIS	7	277	Deionized water, pH 7.0, MICRODIALYSIS, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.74	55.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 49.472	α = 90
b = 77.69	β = 90
c = 143.462	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	RIGAKU JUPITER 210		2005-10-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL32B2	1.0000	SPring-8	BL32B2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.2	50	98.9	0.08	0.091	10.2	4.7	28426	28426		-3	42.361

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.32	99.7		0.669	0.753	2.6	4.8	4116

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1H3X	2.2	50	-3	28378	26944	1434	98.26	0.19483	0.19483	0.19195	0.25064	RANDOM	37.021

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]
-3.25			-0.4		3.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.701
r_dihedral_angle_4_deg	21.168
r_dihedral_angle_3_deg	18.103
r_dihedral_angle_1_deg	7.874
r_scangle_it	4.747
r_scbond_it	3.429
r_angle_refined_deg	2.593
r_mcangle_it	2.079
r_mcbond_it	1.688
r_angle_other_deg	1.104
r_symmetry_vdw_refined	0.511
r_mcbond_other	0.424
r_symmetry_vdw_other	0.302
r_nbd_refined	0.243
r_symmetry_hbond_refined	0.228
r_nbd_other	0.206
r_nbtor_refined	0.195
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.156
r_nbtor_other	0.105
r_bond_refined_d	0.033
r_gen_planes_refined	0.013
r_bond_other_d	0.001
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_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3348
Nucleic Acid Atoms
Solvent Atoms	108
Heterogen Atoms	164

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
PHASER	phasing