2ZJI | pdb_00002zji

Crystal structure of the human BACE1 catalytic domain in complex with N-[1-(2,6-dimethoxy-benzyl)-piperidin-4-yl]-4-mercapto-butyramide

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2P8H	PDB ENTRY 2P8H

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		295	2.0M sodium formate, VAPOR DIFFUSION, SITTING DROP, temperature 295K

Crystal Properties
Matthews coefficient	Solvent content
2.86	57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.306	α = 90
b = 103.306	β = 90
c = 168.014	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	180	IMAGE PLATE	RIGAKU RAXIS IV		2003-12-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU300	1.54

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	2.3	20	100	0.078				24184

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	2.3	2.38			0.357

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2P8H	2.3	20	22764	1244	99.25	0.2355	0.23394	0.22	0.26376	0.25	RANDOM	34.675

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]
-0.27	-0.14		-0.27		0.41

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.417
r_dihedral_angle_3_deg	14.738
r_dihedral_angle_4_deg	12.009
r_dihedral_angle_1_deg	4.97
r_mcangle_it	2.048
r_scangle_it	1.542
r_mcbond_it	1.181
r_scbond_it	0.95
r_angle_refined_deg	0.883
r_nbtor_refined	0.3
r_nbd_refined	0.153
r_symmetry_vdw_refined	0.123
r_xyhbond_nbd_refined	0.093
r_symmetry_hbond_refined	0.082
r_chiral_restr	0.056
r_bond_refined_d	0.006
r_gen_planes_refined	0.002
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	2892
Nucleic Acid Atoms
Solvent Atoms	232
Heterogen Atoms	24

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing