6MG5 | pdb_00006mg5

Structure of full-length human lambda-6A light chain JTO in complex with coumarin 1

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		296	Crystals of JTO-FL were grown via sitting-drop vapor diffusion using a crystallization buffer consisting of 20% PEG 3350 and 0.2 M NH4H2PO4 at 23 degrees C. Both diamond-shaped and plate-shaped crystals were generated in the same drop using these conditions, but only the plate-shaped crystals produced usable diffraction data. To generate JTO-FL:ligand complexes, crystals of apo JTO-FL were soaked with a tenfold molar excess of ligand for 10 days. Crystals were harvested and immediately flash cooled in liquid nitrogen.

Crystal Properties
Matthews coefficient	Solvent content
2.77	55.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.07	α = 90
b = 84.219	β = 90
c = 96.171	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	80	PIXEL	DECTRIS EIGER X 16M		2018-04-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-B	1.0332	APS	23-ID-B

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym I (Observed)	Rpim I (All)	CC (Half)	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	1.8	45.1	98	0.11	0.051	1	9.5	5.2		47842			25

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.8	1.85	95.9		1.59	0.76	0.46	1	5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.8	45.09	44684	2312	96.04	0.207	0.204	0.21	0.263	0.27	RANDOM	35

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]
-0.82			3.03		-2.22

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.347
r_dihedral_angle_4_deg	16.219
r_dihedral_angle_3_deg	13.662
r_long_range_B_refined	7.75
r_long_range_B_other	7.749
r_dihedral_angle_1_deg	7.342
r_scangle_other	5.163
r_mcangle_it	4.464
r_mcangle_other	4.464
r_scbond_it	3.443
r_scbond_other	3.442
r_mcbond_it	2.874
r_mcbond_other	2.874
r_angle_refined_deg	1.401
r_angle_other_deg	0.519
r_chiral_restr	0.061
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3257
Nucleic Acid Atoms
Solvent Atoms	493
Heterogen Atoms	27

Software

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