4RCD | pdb_00004rcd

Crystal structure of BACE1 in complex with a 2-aminooxazoline 4-azaxanthene inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6.6	298	21% polyethylene glycol 5000 monomethyl ether, 180 mM sodium citrate, pH 6.6, 200 mM ammonium iodide, VAPOR DIFFUSION, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.607	α = 90
b = 102.607	β = 90
c = 170.671	γ = 120

Symmetry
Space Group	P 61 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	98	IMAGE PLATE	RIGAKU RAXIS IV++	Varimax HR	2010-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E SUPERBRIGHT	1.5418

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	1.9	30	99.1	0.097	17.5	6.9	42560	42177		-3	32

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	1.9	1.97	94		0.451		3.1	3912

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	1.9	30	42501	42110	2121	99.08	0.2157	0.2139	0.2144	0.251	0.2519	RANDOM	30.512

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]
0.08	0.04		0.08		-0.11

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.995
r_dihedral_angle_4_deg	14.868
r_dihedral_angle_3_deg	12.514
r_dihedral_angle_1_deg	6.474
r_angle_refined_deg	1.21
r_angle_other_deg	0.811
r_chiral_restr	0.068
r_bond_refined_d	0.008
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2898
Nucleic Acid Atoms
Solvent Atoms	370
Heterogen Atoms	48

Software

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