3DHP | pdb_00003dhp

Probing the role of aromatic residues at the secondary saccharide binding sites of human salivary alpha-amylase in substrate hydrolysis and bacterial binding

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	9	298	MPD, pH 9.0, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.736	α = 90
b = 73.722	β = 90
c = 134.095	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	77	CCD	ADSC QUANTUM 4	Mirrors	2007-11-18		SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.9777	CHESS	F1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.5	50	99.4	0.102	0.102	15.8	6.3		84017	3	3	29.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.5	1.53	100		0.368	0.368	3.7	4.8	4171

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	PDB ENTRY 1SMD	1.5	30.95	83812	83812	4199	99.23	0.17	0.17	0.169	0.17	0.186	0.19	RANDOM	23.66

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
r_dihedral_angle_2_deg	35.666
r_dihedral_angle_4_deg	18.036
r_dihedral_angle_3_deg	11.705
r_dihedral_angle_1_deg	5.865
r_scangle_it	3.239
r_scbond_it	2.163
r_mcangle_it	1.41
r_angle_refined_deg	1.329
r_mcbond_it	0.782
r_chiral_restr	0.096

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.666
r_dihedral_angle_4_deg	18.036
r_dihedral_angle_3_deg	11.705
r_dihedral_angle_1_deg	5.865
r_scangle_it	3.239
r_scbond_it	2.163
r_mcangle_it	1.41
r_angle_refined_deg	1.329
r_mcbond_it	0.782
r_chiral_restr	0.096
r_bond_refined_d	0.011
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3932
Nucleic Acid Atoms
Solvent Atoms	444
Heterogen Atoms	46

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.