3UPC | pdb_00003upc

A general strategy for the generation of human antibody variable domains with increased aggregation resistance

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3QOS	PDB ENTRY 3QOS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	counter diffusion in Crystal Harp capillary	5.5	293	20% PEG 3350, 100mM Citrate, pH 5.5, counter diffusion in Crystal Harp capillary, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.55	65.39

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.61	α = 90
b = 143.12	β = 90
c = 145.61	γ = 90

Symmetry
Space Group	P 21 21 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 QUANTUM 315r		2011-09-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.95369	Australian Synchrotron	MX2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.8	145.61	100	0.151	10.5	7.2	43312	43312	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.95	100		0.777	0.777	0.836	0.306	1	7.4	6259

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 3QOS	2.8	145.61	43273	43273	2180	99.94	0.2112	0.2112	0.2093	0.21	0.247	0.24	RANDOM	40.975

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]
-2.96			2.5		0.46

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.254
r_dihedral_angle_4_deg	20.768
r_dihedral_angle_3_deg	13.938
r_dihedral_angle_1_deg	10.322
r_angle_refined_deg	1.452
r_angle_other_deg	0.929
r_chiral_restr	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.254
r_dihedral_angle_4_deg	20.768
r_dihedral_angle_3_deg	13.938
r_dihedral_angle_1_deg	10.322
r_angle_refined_deg	1.452
r_angle_other_deg	0.929
r_chiral_restr	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8129
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	88

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Blu-Ice	data collection

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.