3M07

1.4 Angstrom Resolution Crystal Structure of Putative alpha Amylase from Salmonella typhimurium.

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.5	295	Protein solution: 8.1 mG/mL, 0.25M Sodium chloride, 0.01M Tris-HCl (pH 8.3); Screen solution: JCSG+, H11, 0.2M Magnesium chloride, 0.1M bis-Tris (pH 5.5), 25% w/v PEG 3350., VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
1.83	32.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 174.048	α = 90
b = 51.534	β = 101.18
c = 57.014	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	MARMOSAIC 300 mm CCD	Beryllium lenses	2010-02-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97856	APS	21-ID-G

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	1.4	30	99.5	0.039	28.1	3.7	97228	97228		-3	17.5

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)
	1.4	1.42	96.3		0.378	2.9	2.9	4685

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	2BHZ	1.4	29.79	92329	92329	4852	99.49	0.14913	0.14913	0.14789	0.17265	RANDOM	17.269

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]
-0.37		0.24	0.3		0.16

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.11
r_dihedral_angle_4_deg	11.844
r_dihedral_angle_3_deg	11.544
r_dihedral_angle_1_deg	4.489
r_scangle_it	4.072
r_scbond_it	2.667
r_mcangle_it	2.137
r_angle_refined_deg	1.448
r_mcbond_it	1.265
r_angle_other_deg	0.883

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.11
r_dihedral_angle_4_deg	11.844
r_dihedral_angle_3_deg	11.544
r_dihedral_angle_1_deg	4.489
r_scangle_it	4.072
r_scbond_it	2.667
r_mcangle_it	2.137
r_angle_refined_deg	1.448
r_mcbond_it	1.265
r_angle_other_deg	0.883
r_mcbond_other	0.371
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.007
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4963
Nucleic Acid Atoms
Solvent Atoms	661
Heterogen Atoms	60

Software

Software
Software Name	Purpose
Blu-Ice	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.