3HVG | pdb_00003hvg

Structure of bace (beta secretase) in Complex with EV0

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	293	10% PEG 4000, 100mM MES pH 6.0, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 232.55	α = 90
b = 100.13	β = 103.73
c = 64.78	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	1.000	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	2.25	48.34	97.2	0.045	0.045	13.26	3	66620	66428	2	2	29.654

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	2.25	2.44	89.9		0.347	0.347	2.65	2.3	13253

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 (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	2.26	48.34	2	2	66620	63110	3318	100	0.22456	0.22245	0.29	0.26487	0.32	RANDOM	29.654

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]
-5.87		-1.19	-1.46		6.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.067
r_dihedral_angle_4_deg	19.241
r_dihedral_angle_3_deg	14.154
r_dihedral_angle_1_deg	6.725
r_scangle_it	1.734
r_scbond_it	1.221
r_angle_refined_deg	1.154
r_mcangle_it	0.918
r_angle_other_deg	0.732
r_mcbond_it	0.719
r_symmetry_vdw_refined	0.269
r_symmetry_vdw_other	0.209
r_nbd_refined	0.181
r_nbtor_refined	0.178
r_nbd_other	0.169
r_xyhbond_nbd_refined	0.154
r_mcbond_other	0.118
r_xyhbond_nbd_other	0.117
r_symmetry_hbond_refined	0.102
r_nbtor_other	0.08
r_chiral_restr	0.068
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8830
Nucleic Acid Atoms
Solvent Atoms	180
Heterogen Atoms	39

Software

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