3SKF | pdb_00003skf

Crystal structure of beta-site app-cleaving enzyme 1 (BACE-WT) complex with (2S)-2-((3S)-3-(acetylamino)-3-(butan-2-yl)-2-oxopyrrolidin-1-yl)-N-((2S,3R)-3-hydroxy-4-((3-methoxybenzyl)amino)-1-phenylbutan-2-yl)-4-phenylbutanamide

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	298	pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.07

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.288	α = 90
b = 130.264	β = 90
c = 85.871	γ = 90

Symmetry
Space Group	P 21 21 2

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	2003-09-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E DW

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	3	34.06	99.9	0.229	3.4	7.2		20761

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	3	3.11	100			7.2	2057

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	3	34.06	20703	1064	99.42	0.2555	0.2523	0.2524	0.3133	0.3071	RANDOM	31.7743

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]
5.07			-2.3		-2.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.742
r_dihedral_angle_3_deg	21.102
r_dihedral_angle_4_deg	15.275
r_dihedral_angle_1_deg	6.468
r_angle_refined_deg	1.309
r_scangle_it	1.268
r_scbond_it	0.725
r_mcangle_it	0.413
r_nbtor_refined	0.317
r_symmetry_hbond_refined	0.242

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.742
r_dihedral_angle_3_deg	21.102
r_dihedral_angle_4_deg	15.275
r_dihedral_angle_1_deg	6.468
r_angle_refined_deg	1.309
r_scangle_it	1.268
r_scbond_it	0.725
r_mcangle_it	0.413
r_nbtor_refined	0.317
r_symmetry_hbond_refined	0.242
r_symmetry_vdw_refined	0.231
r_nbd_refined	0.224
r_mcbond_it	0.201
r_xyhbond_nbd_refined	0.157
r_chiral_restr	0.089
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6077
Nucleic Acid Atoms
Solvent Atoms	188
Heterogen Atoms	96

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
HKL-2000	data reduction
HKL-2000	data scaling
EPMR	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.