1PEW | pdb_00001pew

High Resolution Crystal Structure of Jto2, a mutant of the non-amyloidogenic Lamba6 Light Chain, Jto

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1CD0	PDB ENTRY 1CD0

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5	298	0.1M Na Acetate, 0.8M Amm. Sulfate, 100mM Cadmium chloride, 10% n-Decyl-B-D-maltoside, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.54	51.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.577	α = 90
b = 73.577	β = 90
c = 92.298	γ = 90

Symmetry
Space Group	P 41 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	113	DIFFRACTOMETER	RIGAKU AFC-5R		2001-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	MPG/DESY, HAMBURG BEAMLINE BW6	1.5418	MPG/DESY, HAMBURG	BW6

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	1.6	15	97.3	0.066	20.2	13.3	32368	31495		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	1.6	1.66	93.8		0.515	5.4	11.3	3339

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 ENTRY 1CD0	1.6	8	4	31495	1633	97.3	0.295	0.2533	0.2522	0.287	0.27291	0.2958	RANDOM	12.751

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]
0.14			0.14		-0.28

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.962
r_scangle_it	2.234
r_scbond_it	1.565
r_angle_refined_deg	1.29
r_mcangle_it	0.904
r_mcbond_it	0.53
r_symmetry_hbond_refined	0.352
r_symmetry_vdw_refined	0.334
r_xyhbond_nbd_other	0.234
r_nbd_refined	0.228
r_xyhbond_nbd_refined	0.208
r_chiral_restr	0.082
r_bond_refined_d	0.017
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1647
Nucleic Acid Atoms
Solvent Atoms	104
Heterogen Atoms	4

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement