5A2C | pdb_00005a2c

Crystal Structure of Anoxybacillus Alpha-amylase Provides Insights into a New Glycosyl Hydrolase Subclass

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4E2O

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.5		THE TASKA-MALTODP3 NAMELY TASKA-T COMPLEXES WAS CRYSTALLIZED USING THE STREAK SEEDING METHOD WITH A COMMERCIALLY AVAILABLE SEEDING TOOL, HAMPTON RESEARCH, USA. THE SEEDING TOOL WAS DIPPED INTO A DROP CONTAINING TASKA-APO,PDB ID 5A2A, CRYSTALS AND STREAKED ON THE DROPS THAT CONSISTED OF 0.3 UL 6 MG/ML TASKA PROTEIN AND 0.3 UL RESERVOIR SOLUTION 0.1 M CALCIUM ACETATE, 0.1 M SODIUM CACODYLATE PH 6.5, AND 18 % W/V POLYETHYLENE GLYCOL 8,000 WITH 20 MM MALTOTRIOSE.

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.816	α = 90
b = 63.532	β = 90
c = 122.97	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	IMAGE PLATE	RIGAKU R-AXIS IV		2014-07-10	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007 HF

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge 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	1.9	19.54	96.7	0.09	12.6	3.6		37601		1.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.94	86.6		0.58	1.9	2.9

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	4E2O	1.9	61.49	35690	1861	96.39	0.1585	0.15585	0.17	0.20914	0.21	RANDOM	21.102

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]
-0.54			-0.63		1.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.821
r_dihedral_angle_4_deg	15.418
r_dihedral_angle_3_deg	14.061
r_dihedral_angle_1_deg	6.138
r_scbond_it	1.991
r_mcangle_it	1.875
r_angle_refined_deg	1.821
r_mcbond_it	1.292
r_mcbond_other	1.284
r_angle_other_deg	0.884
r_chiral_restr	0.115
r_bond_refined_d	0.018
r_gen_planes_refined	0.01
r_bond_other_d	0.002
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_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3756
Nucleic Acid Atoms
Solvent Atoms	518
Heterogen Atoms	27

Software

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