4NY6 | pdb_00004ny6

Neutron structure of leucine and valine methyl protonated type III antifreeze

NEUTRON DIFFRACTION - X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.2	285	10mg/ml protein in 50 mM sodium acetate pD 5.2. Drops containing 20 ml protein solution and 30 ml precipitant buffer (2.1 M ammonium sulfate, 9% d8-glycerol) were equilibrated against 1 ml precipitant buffer in the reservoir, VAPOR DIFFUSION, SITTING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
2.16	43.08

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 32.73	α = 90
b = 39.12	β = 90
c = 46.54	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	PIXEL	DECTRIS PILATUS 6M			M	SINGLE WAVELENGTH
2	1	neutron	298	LADI-III	Image Plate		2008-05-28	L	LAUE

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-1	0.6525	ESRF	ID23-1
2	NUCLEAR REACTOR	OTHER	3.18-4.22

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	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	1.05	50	99.7	0.048						32.5	6.1		28534
2	1.8	46.52	89.3	0.136						14	11.1	5916	5194

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	R Split (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.05	1.09		0.638						2.66
2	1.8	1.9		0.169						6.6	3.5

Refinement

Statistics
Diffraction ID	Structure Solution Method	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		1.05	18.965		1.34		28511	1426	99.82		0.1712	0.1703	0.1706	0.1881	0.188		16.9609
NEUTRON DIFFRACTION		1.85	26.772				4897	246	89.94		0.1782	0.1757		0.2245

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]

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	15.259
f_angle_d	1.302
f_chiral_restr	0.08
f_bond_d	0.013
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	479
Nucleic Acid Atoms
Solvent Atoms	42
Heterogen Atoms

Software

Software
Software Name	Purpose
QLD	data collection
PHENIX	model building
PHENIX	refinement
LAUEGEN	data reduction
LSCALE	data scaling
SCALA	data scaling
PHENIX	phasing