4FSE | pdb_00004fse

crystal structure of beta-site app-cleaving enzyme 1 (bace-wt) complex with N-(N-(4-amino-3,5- dichlorobenzyl)carbamimidoyl)-3-(4-methoxyphenyl)-5- methyl-4-isothiazolecarboxamide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	298	35% PEG8K, 0.2 M ammonium sulfate, pH 6.2, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.49	50.52

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.334	α = 90
b = 131.219	β = 97.6
c = 88.947	γ = 90

Symmetry
Space Group	P 1 21 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	RIGAKU SATURN 92	MICROMAX CONFOCAL	2005-04-29	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.54

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	2.65	50	99.8	0.135	5.5	3.7		56952

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	2.65	2.74	99		0.49		3.5	5619

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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	2.65	44.08	56926	2884	99.76	0.2196	0.2171	0.2172	0.2669	0.266	RANDOM	20.8044

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]
-1.67		0.16	-1.62		3.33

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.297
r_dihedral_angle_3_deg	15.56
r_dihedral_angle_4_deg	15.099
r_dihedral_angle_1_deg	5.927
r_scangle_it	1.562
r_angle_refined_deg	1.364
r_scbond_it	0.935
r_mcangle_it	0.8
r_mcbond_it	0.431
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.297
r_dihedral_angle_3_deg	15.56
r_dihedral_angle_4_deg	15.099
r_dihedral_angle_1_deg	5.927
r_scangle_it	1.562
r_angle_refined_deg	1.364
r_scbond_it	0.935
r_mcangle_it	0.8
r_mcbond_it	0.431
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.288
r_nbd_refined	0.194
r_symmetry_hbond_refined	0.192
r_xyhbond_nbd_refined	0.153
r_chiral_restr	0.091
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	12146
Nucleic Acid Atoms
Solvent Atoms	435
Heterogen Atoms	129

Software

Software
Software Name	Purpose
REFMAC	refinement
CNS	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
StructureStudio	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

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.