8H8Q | pdb_00008h8q

Fab-amyloid beta fragment complex at neutral pH

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	7E6P

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.2	293	PEG3350, magnesium chloride, HEPES pH 7.2

Crystal Properties
Matthews coefficient	Solvent content
2.2	44.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 40.04	α = 90
b = 94.15	β = 90
c = 115.44	γ = 90

Symmetry
Space Group	P 21 21 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	PIXEL	DECTRIS PILATUS 6M		2021-05-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL45XU	1.0000	SPring-8	BL45XU

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	CC (Half)	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	2.5	72.961	100	0.983	9.1	35.1		15801

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.5	2.55			0.739

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	7E6P	2.5	49.257	15753	803	99.987	0.215	0.2125	0.22	0.2745	0.28	1	18.246

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]
-0.306			-0.432		0.737

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	10.935
r_dihedral_angle_3_deg	9.674
r_dihedral_angle_1_deg	5.704
r_lrange_it	4.216
r_lrange_other	4.214
r_mcangle_it	2.484
r_mcangle_other	2.484
r_scangle_it	2.326
r_scangle_other	2.325
r_mcbond_it	1.437
r_mcbond_other	1.436
r_scbond_it	1.427
r_scbond_other	1.426
r_dihedral_angle_2_deg	1.298
r_angle_refined_deg	0.511
r_angle_other_deg	0.399
r_symmetry_nbd_other	0.241
r_nbd_other	0.217
r_symmetry_xyhbond_nbd_refined	0.21
r_nbd_refined	0.205
r_symmetry_nbd_refined	0.185
r_nbtor_refined	0.18
r_xyhbond_nbd_refined	0.136
r_symmetry_nbtor_other	0.089
r_chiral_restr	0.027
r_gen_planes_other	0.017
r_gen_planes_refined	0.013
r_bond_other_d	0.002
r_bond_refined_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3386
Nucleic Acid Atoms
Solvent Atoms	72
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling
MOLREP	phasing