1W50

Apo Structure of BACE (Beta Secretase)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FKN	PDB ENTRY 1FKN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		6.6		pH 6.60

Crystal Properties
Matthews coefficient	Solvent content
2.86	56.65

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.243	α = 90
b = 103.243	β = 90
c = 169.108	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	100	CCD	ADSC CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	1.75	39.5	95.9	0.1	4.6	6.3		51594

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	1.75	1.84	97.2		0.45	1.7

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1FKN	1.75	39.52	48964	2624	95.1	0.245	0.244	0.283	RANDOM	30.01

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]
-0.53	-0.26		-0.53		0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	7.215
r_scangle_it	5.221
r_mcangle_it	4.075
r_scbond_it	3.752
r_mcbond_it	2.943
r_angle_refined_deg	1.427
r_angle_other_deg	0.84
r_symmetry_vdw_other	0.29
r_nbd_other	0.24
r_symmetry_vdw_refined	0.221
r_nbd_refined	0.219
r_xyhbond_nbd_refined	0.218
r_symmetry_hbond_refined	0.181
r_nbtor_other	0.086
r_chiral_restr	0.084
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_nbtor_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2966
Nucleic Acid Atoms
Solvent Atoms	279
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
EPMR	phasing