3IXJ | pdb_00003ixj

Crystal structure of beta-secretase 1 in complex with selective beta-secretase 1 inhibitor

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5	299	16% PEG 8000, 0.1M CITRATE, 0.3M LITHIUM SULFATE, 0.1M SODIUM CHLORIDE, pH 5.0, VAPOR DIFFUSION, temperature 299K

Crystal Properties
Matthews coefficient	Solvent content
3.17	61.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 81.913	α = 90
b = 102.705	β = 103.42
c = 100.417	γ = 90

Symmetry
Space Group	P 1 21 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	ADSC QUANTUM 210			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)	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	2.2	62.994	100	0.099	0.099	6.2	4		82125

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)
	2.2	2.32	100		0.31	0.31	2.5	4

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	2.2	62.99	81771	4101	99.5	0.213	0.212	0.2107	0.243	0.2423	RANDOM	19.74

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]
0.06		0.11	0.25		-0.25

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.971
r_dihedral_angle_4_deg	15.447
r_dihedral_angle_3_deg	12.912
r_dihedral_angle_1_deg	5.937
r_scangle_it	3.249
r_scbond_it	2.169
r_mcangle_it	1.591
r_angle_refined_deg	1.128
r_mcbond_it	1.067
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.204
r_nbd_refined	0.173
r_symmetry_hbond_refined	0.167
r_xyhbond_nbd_refined	0.104
r_chiral_restr	0.075
r_bond_refined_d	0.011
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8805
Nucleic Acid Atoms
Solvent Atoms	241
Heterogen Atoms	195

Software

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