2Q20 | pdb_00002q20

Structure of the germline Vk1 O18/O8 light chain variable domain homodimer

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1BRE	polyserine model of pdb entry 1BRE chain A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		295	Protein: 890 micromolar in 10 mM TRIS pH 7.4. Mother Liquor: 15-30% (w/v) PEG 4K, 0.2 Li2SO4, 0.1 M TRIS pH 7.9-8.9, VAPOR DIFFUSION, HANGING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.63

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.265	α = 90
b = 74.265	β = 90
c = 99.051	γ = 120

Symmetry
Space Group	P 61

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	SBC-3	mirror	2007-02-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	1.0718	APS	19-BM

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.3	99	99.7	0.046	53.2	12.2	74839	74839			22.2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.3	1.33	96.3		0.53	2.3	5.6	5311

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	polyserine model of pdb entry 1BRE chain A	1.3	99	74839	74839	535	99.19	0.11955	0.11935	0.12	0.14815	0.15	RANDOM	14.491

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]
0.06	0.03		0.06		-0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.932
r_dihedral_angle_4_deg	19.808
r_sphericity_free	16.821
r_dihedral_angle_3_deg	11.163
r_dihedral_angle_1_deg	6.402
r_scangle_it	5.511
r_scbond_it	4.5
r_sphericity_bonded	4.388
r_mcangle_it	2.977
r_mcbond_it	2.459
r_rigid_bond_restr	2.333
r_angle_other_deg	2.164
r_angle_refined_deg	1.773
r_mcbond_other	1.682
r_xyhbond_nbd_refined	0.301
r_nbd_refined	0.265
r_symmetry_vdw_other	0.232
r_nbd_other	0.225
r_symmetry_hbond_refined	0.224
r_nbtor_refined	0.193
r_symmetry_vdw_refined	0.132
r_chiral_restr	0.117
r_nbtor_other	0.091
r_xyhbond_nbd_other	0.062
r_bond_refined_d	0.019
r_gen_planes_refined	0.009
r_gen_planes_other	0.007
r_bond_other_d	0.003
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1970
Nucleic Acid Atoms
Solvent Atoms	454
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SBC-Collect	data collection
HKL-3000	data reduction
HKL-3000	data scaling
PHASER	phasing