1MFU | pdb_00001mfu

Probing the role of a mobile loop in human salivary amylase: Structural studies on the loop-deleted mutant

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1JXK	PDB entry 1jxk

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	soaking with acarbose at 1 mM concentration for 24 hours	9	298	40% mpd, pH 9.0, soaking with acarbose at 1 mM concentration for 24 hours, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.34	47.53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.074	α = 90
b = 73.815	β = 90
c = 135.787	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	CCD	ADSC QUANTUM 4	monochromator	2002-03-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CHESS BEAMLINE F1	0.91	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	2	26.54	96.8	0.06	0.06	24.5	4.8	35031	35031	1	1	25.6

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)
	2	2.07			0.267	0.267	7		3488

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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1jxk	2	26.54	35031	33226	1746	96.86	0.1622	0.16226	0.16011	0.16	0.20109	0.21	RANDOM	25.789

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_1_deg	6.254
r_scangle_it	2.997
r_scbond_it	2.041
r_angle_refined_deg	1.368
r_mcangle_it	1.265
r_mcbond_it	0.691
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.199
r_symmetry_hbond_refined	0.142
r_xyhbond_nbd_refined	0.139

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.254
r_scangle_it	2.997
r_scbond_it	2.041
r_angle_refined_deg	1.368
r_mcangle_it	1.265
r_mcbond_it	0.691
r_nbd_refined	0.2
r_symmetry_vdw_refined	0.199
r_symmetry_hbond_refined	0.142
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.096
r_metal_ion_refined	0.077
r_bond_refined_d	0.013
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3924
Nucleic Acid Atoms
Solvent Atoms	290
Heterogen Atoms	199

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement

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.