Experiment: 4GKL

Crystal structure of a noncanonic maltogenic alpha-amylase AmyB from Thermotoga neapolitana

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3DHU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	287	0.1M Sodium acetate, 2M sodium formate , pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 287K

Crystal Properties
Matthews coefficient	Solvent content
2.58	52.25

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.88	α = 90
b = 74.449	β = 107.77
c = 108.9	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	173	CCD	ADSC QUANTUM 210r		2011-10-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PHOTON FACTORY BEAMLINE AR-NE3A	1.0	Photon Factory	AR-NE3A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.4	20	94.1			37665	35640

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.44	86.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	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	3DHU	2.4	19.98	1.54	37665	35640	1981	93.93	0.201	0.1974	0.1983	0.2633	0.2637	RANDOM

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]
7.3982		10.6891	-11.9694		4.5713

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.052
f_angle_d	1.278
f_chiral_restr	0.091
f_bond_d	0.008
f_plane_restr	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7021
Nucleic Acid Atoms
Solvent Atoms	244
Heterogen Atoms

Software

Software
Software Name	Purpose
HKL-2000	data collection
CCP4	model building
PHENIX	refinement
DENZO	data reduction
HKL-2000	data scaling
CCP4	phasing