2OHS | pdb_00002ohs

X-ray crystal structure of beta secretase complexed with compound 6b

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1W50	PDB entry 1W50

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.6	293	20-22.5% (w/v) PEG 5000 monomethylether (MME), 200 mM sodium citrate (pH 6.6), 200 mM ammonium iodide, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.81	56.26

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 101.303	α = 90
b = 101.303	β = 90
c = 170.355	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	MAR CCD 165 mm		2004-02-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-3	0.93100	ESRF	ID14-3

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	2.45	50.65	95.8	0.118			18681	18681

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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 1W50	2.45	50.65	18681	18681	947	94.89	0.185	0.185	0.182	0.1876	0.251	0.2522	RANDOM	24.868

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]
-0.93	-0.46		-0.93		1.39

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.052
r_dihedral_angle_4_deg	17.123
r_dihedral_angle_3_deg	16.474
r_dihedral_angle_1_deg	6.872
r_angle_refined_deg	1.478
r_angle_other_deg	0.988
r_symmetry_vdw_other	0.254
r_nbd_refined	0.208
r_nbd_other	0.205
r_symmetry_vdw_refined	0.197
r_nbtor_refined	0.191
r_xyhbond_nbd_refined	0.185
r_chiral_restr	0.154
r_scangle_it	0.127
r_symmetry_hbond_refined	0.118
r_scbond_it	0.1
r_mcangle_it	0.091
r_nbtor_other	0.089
r_mcbond_it	0.062
r_mcbond_other	0.022
r_bond_refined_d	0.013
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	2948
Nucleic Acid Atoms
Solvent Atoms	209
Heterogen Atoms	48

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
ProDC	data collection
MOSFLM	data reduction
CCP4	data scaling
CSearch	phasing