5MP5 | pdb_00005mp5

Crystal structure of DC8E8 Fab in the complex with a 14-mer tau peptide at pH 6.5

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4OZ4	pdbid 4OZ4

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	295	20% PEG 8000, 0.1 M Na-cacodylate, 0.2 M Mg-acetate

Crystal Properties
Matthews coefficient	Solvent content
2.26	45.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.75	α = 92.35
b = 82.12	β = 95.36
c = 89.04	γ = 89.86

Symmetry
Space Group	P 1

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	MARMOSAIC 225 mm CCD		2008-08-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	1.0000	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.31	34.5	96.6	0.048	0.997	14.86	2.095		64648		-3	39.915

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.46	96.4		0.338	0.706	2.54	2.047

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	pdbid 4OZ4	2.31	34.5	61485	3165	85.74	0.2368	0.2348	0.27	0.2765	0.32	RANDOM	37.366

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]
5.74	6.2	-3.88	-7.12	-1.54	1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.576
r_dihedral_angle_4_deg	17.613
r_dihedral_angle_3_deg	14.98
r_dihedral_angle_1_deg	6.946
r_angle_refined_deg	1.521
r_angle_other_deg	1.314
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.005

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.576
r_dihedral_angle_4_deg	17.613
r_dihedral_angle_3_deg	14.98
r_dihedral_angle_1_deg	6.946
r_angle_refined_deg	1.521
r_angle_other_deg	1.314
r_chiral_restr	0.074
r_bond_refined_d	0.01
r_gen_planes_refined	0.007
r_bond_other_d	0.005
r_gen_planes_other	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13382
Nucleic Acid Atoms
Solvent Atoms	123
Heterogen Atoms

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.