3HW1 | pdb_00003hw1

Structure of Bace (beta secretase) in complex with ligand EV2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2B8L	PDB ENTRY 2B8L

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	6	295	10% PEG 4000, 100mM MES pH 6.0, VAPOR DIFFUSION, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.1

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 230.625	α = 90
b = 99.88	β = 103.12
c = 62.9	γ = 90

Symmetry
Space Group	C 1 2 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	MARMOSAIC 225 mm CCD		2008-01-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.9999	SLS	X06DA

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	2.48	48.8	98.3	0.047	0.047	14.82	3.3	47564	48552	2	2	20.736

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)
1	2.48	2.57	96.2		0.657	0.657	3.01	3.2	4849

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Cut-off Sigma (F)	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 2B8L	2.48	48.8	2	2	48570	47564	986	100	0.22703	0.226	0.22585	0.23	0.28115	0.28	RANDOM	20.736

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]
-7.7		-0.13	-5.13		12.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.663
r_dihedral_angle_4_deg	20.226
r_dihedral_angle_3_deg	15.73
r_dihedral_angle_1_deg	6.727
r_scangle_it	2.145
r_scbond_it	1.45
r_angle_refined_deg	1.21
r_angle_other_deg	1.17
r_mcangle_it	1.075
r_mcbond_it	0.869
r_symmetry_vdw_other	0.281
r_nbd_other	0.192
r_symmetry_vdw_refined	0.191
r_nbd_refined	0.189
r_nbtor_refined	0.183
r_xyhbond_nbd_refined	0.156
r_symmetry_hbond_refined	0.104
r_mcbond_other	0.093
r_nbtor_other	0.083
r_chiral_restr	0.071
r_bond_refined_d	0.01
r_gen_planes_refined	0.004
r_xyhbond_nbd_other	0.004
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8784
Nucleic Acid Atoms
Solvent Atoms	117
Heterogen Atoms	54

Software

Software
Software Name	Purpose
SLSPX	data collection
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling