2VA7 | pdb_00002va7

X-ray crystal structure of beta secretase complexed with compound 27

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

Crystal Properties
Matthews coefficient	Solvent content
3.07	51.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 102.687	α = 90
b = 102.687	β = 90
c = 168.34	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 ID14-3		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	2.2	47	99.9	0.07		2.5		25942

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	2.2	2.26	100		0.42

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 1W50	2.2	47.46	25942	1378	99.9	0.226	0.223	0.2282	0.28	0.282	RANDOM	33.39

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]
-0.25	-0.12		-0.25		0.37

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.125
r_dihedral_angle_3_deg	17.205
r_dihedral_angle_4_deg	16.501
r_dihedral_angle_1_deg	7.999
r_angle_refined_deg	1.493
r_angle_other_deg	0.902
r_symmetry_vdw_other	0.281
r_symmetry_vdw_refined	0.222
r_symmetry_hbond_refined	0.22
r_xyhbond_nbd_refined	0.211
r_nbd_other	0.208
r_nbd_refined	0.202
r_nbtor_refined	0.189
r_scangle_it	0.111
r_scbond_it	0.094
r_nbtor_other	0.093
r_mcangle_it	0.093
r_chiral_restr	0.088
r_mcbond_it	0.069
r_bond_refined_d	0.015
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
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	2948
Nucleic Acid Atoms
Solvent Atoms	203
Heterogen Atoms	29

Software

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