4HBC | pdb_00004hbc

Crystal structure of a conformation-dependent rabbit IgG Fab specific for amyloid prefibrillar oligomers

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	0.2 M Magnesium sulfate 20 % PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.41	49.06

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.934	α = 90
b = 42.184	β = 114.93
c = 86.179	γ = 90

Symmetry
Space Group	C 1 2 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	ADSC QUANTUM 315r		2007-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-1	0.979462	SSRL	BL9-1

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	1.54	31.01	87.6	0.081	10.2	6.46		56536

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	1.54	1.6	49.7		0.53	2	4.67	3191

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	1.54	31	56401	2857	87.35	0.2004	0.1973	0.19	0.2592	0.26	RANDOM	27.7234

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]
-1.22		-1.19	2.11		-1.88

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.487
r_sphericity_free	28.311
r_dihedral_angle_3_deg	12.169
r_dihedral_angle_4_deg	11.081
r_sphericity_bonded	10.391
r_dihedral_angle_1_deg	6.666
r_rigid_bond_restr	2.655
r_angle_refined_deg	1.507
r_chiral_restr	0.092
r_bond_refined_d	0.012

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.487
r_sphericity_free	28.311
r_dihedral_angle_3_deg	12.169
r_dihedral_angle_4_deg	11.081
r_sphericity_bonded	10.391
r_dihedral_angle_1_deg	6.666
r_rigid_bond_restr	2.655
r_angle_refined_deg	1.507
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3152
Nucleic Acid Atoms
Solvent Atoms	434
Heterogen Atoms	5

Software

Software
Software Name	Purpose
d*TREK	data scaling
d*TREK	data reduction
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.