3MJ8

Crystal structure of HL4E10 Fab, a hamster Ab stimulatory for gammadelta T cells

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W72	HL4E10 LIGHT CHAIN SEQUENCE THREADED ONTO 1W72, HL4E10 HEAVY CHAIN SEQUENCE THREADED ONTO 2ARJ
experimental model	PDB	2ARJ	HL4E10 LIGHT CHAIN SEQUENCE THREADED ONTO 1W72, HL4E10 HEAVY CHAIN SEQUENCE THREADED ONTO 2ARJ

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	4.6	295	10-12.5 % PEG 4000, 0.1 M NA- ACETATE, 0.2 M (NH4)2SO4, pH 4.60, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 43.836	α = 90
b = 148.768	β = 106.23
c = 68.798	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	CCD	MARMOSAIC 325 mm CCD	FLAT MIRROR (VERTICAL FOCUSING), SINGLE CRYSTAL SI(111) BENT MONOCHROMATOR (HORIZONTAL FOCUSING)	2006-07-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	2.94	30	95.3	0.105	0.105	7.7	2.3		17012			70.8

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	2.94	3.06	96.1		0.541	0.541	1.7

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	HL4E10 LIGHT CHAIN SEQUENCE THREADED ONTO 1W72, HL4E10 HEAVY CHAIN SEQUENCE THREADED ONTO 2ARJ	2.94	30	16120	863	94.5	0.23	0.227	0.281	RANDOM	54.67

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]
4.15		-2.78	-1.05		-4.65

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.775
r_dihedral_angle_3_deg	14.298
r_dihedral_angle_4_deg	10.274
r_dihedral_angle_1_deg	5.766
r_angle_refined_deg	0.957
r_angle_other_deg	0.744
r_scangle_it	0.395
r_scbond_it	0.259
r_mcangle_it	0.184
r_nbd_refined	0.178
r_nbtor_refined	0.173
r_nbd_other	0.171
r_mcbond_it	0.148
r_symmetry_hbond_refined	0.133
r_symmetry_vdw_other	0.131
r_xyhbond_nbd_refined	0.129
r_symmetry_vdw_refined	0.125
r_nbtor_other	0.079
r_chiral_restr	0.056
r_mcbond_other	0.021
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
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	6320
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

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