2PH6 | pdb_00002ph6

Crystal Structure of Human Beta Secretase Complexed with inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TQF	pdb entry 1TQF

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	298	1.5M LITHIUM SULFATE, 0.1M HEPES BUFFER, Crystals were grown with L124671 and L304507 was back soak, pH 7.50, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.83	56.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.795	α = 90
b = 127.13	β = 90
c = 76.205	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++		2003-12-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.6	50	87.5	0.083	17.9	3.2		32116

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.6	1.66	35		0.5	1.5

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 (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	pdb entry 1TQF	2	50	32116	1763	98.5	0.19524	0.19402	0.21795	RANDOM	31.045

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]
-1.2			3.52		-2.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.622
r_dihedral_angle_4_deg	23.721
r_dihedral_angle_3_deg	13.572
r_dihedral_angle_1_deg	6.12
r_scangle_it	2.557
r_scbond_it	1.566
r_angle_refined_deg	1.228
r_mcangle_it	1.205
r_mcbond_it	0.719
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.2
r_nbd_refined	0.193
r_symmetry_hbond_refined	0.147
r_xyhbond_nbd_refined	0.118
r_chiral_restr	0.084
r_bond_refined_d	0.01
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	2922
Nucleic Acid Atoms
Solvent Atoms	211
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
REFMAC	phasing