3BCF

Alpha-amylase B from Halothermothrix orenii

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	30% (w/v) monomethylether PEG 5000, 0.1M Mes-OH, 0.2M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
3.19	61.47

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 226.62	α = 90
b = 77.82	β = 99.38
c = 50.33	γ = 90

Symmetry
Space Group	C 1 2 1

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	mirrors	2005-01-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-BM	0.978	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	2	40	98.3	0.106	9.5	4.7	58453	51305

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	2	2.07	99.4		0.308	2.7	5.2	5891

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1VJS	2.3	30	35637	35637	1902	97.47	0.1927	0.1927	0.19076	0.22869	RANDOM	37.79

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]
-0.78		0.11	1.97		-1.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.502
r_dihedral_angle_4_deg	17.635
r_dihedral_angle_3_deg	15.667
r_dihedral_angle_1_deg	6.932
r_scangle_it	3.99
r_scbond_it	2.714
r_mcangle_it	1.8
r_angle_refined_deg	1.796
r_mcbond_it	1.066
r_angle_other_deg	1.008
r_mcbond_other	0.268
r_symmetry_vdw_other	0.255
r_nbd_refined	0.212
r_nbd_other	0.206
r_symmetry_hbond_refined	0.204
r_nbtor_refined	0.196
r_xyhbond_nbd_refined	0.189
r_symmetry_vdw_refined	0.189
r_chiral_restr	0.121
r_nbtor_other	0.093
r_metal_ion_refined	0.086
r_bond_refined_d	0.023
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4747
Nucleic Acid Atoms
Solvent Atoms	256
Heterogen Atoms	5

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data collection
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing