1MFV | pdb_00001mfv

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

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	vapordiffusion, combined with soaking with inhibitor at 1 mM concentration	9	298	40% MPD, pH 9.0, vapordiffusion, combined with soaking with inhibitor at 1 mM concentration, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.27	45.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.681	α = 90
b = 73.197	β = 90
c = 134.448	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	20	96.7	0.091	0.091	32	5.4	34179	34179	1	1	28.1

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)
	2	2.07	98.9		0.37	0.37	5.8

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 code 1smd	2	20	34179	31608	1660	94.48	0.1685	0.16854	0.16709	0.1708	0.19489	0.1984	RANDOM	28.086

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	6.248
r_scangle_it	2.966
r_scbond_it	2.003
r_angle_refined_deg	1.317
r_mcangle_it	1.221
r_mcbond_it	0.661
r_symmetry_vdw_refined	0.203
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.248
r_scangle_it	2.966
r_scbond_it	2.003
r_angle_refined_deg	1.317
r_mcangle_it	1.221
r_mcbond_it	0.661
r_symmetry_vdw_refined	0.203
r_nbd_refined	0.198
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.12
r_chiral_restr	0.096
r_metal_ion_refined	0.02
r_bond_refined_d	0.013
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3946
Nucleic Acid Atoms
Solvent Atoms	243
Heterogen Atoms	100

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.