4ODV | pdb_00004odv

Fab Structure of lipid A-specific antibody A6 in complex with lipid A carbohydrate backbone

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4ODT	PDB ENTRY 4ODT

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	289	0.1M HEPES pH 7.5, 25% (w/v) PEG 3350, VAPOR DIFFUSION, HANGING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
1.95	37.03

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 37.563	α = 90
b = 64.285	β = 90
c = 154.157	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	CCD	MARMOSAIC 300 mm CCD	Vertical focusing mirror	2011-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	CLSI BEAMLINE 08ID-1	0.9794	CLSI	08ID-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	2.15	25	99.7	0.085	12.8	4.9		21071

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	2.15	2.23	99.1		0.404		4.5	2056

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 4ODT	2.15	24.83	21015	1073	99.62	0.2067	0.2044	0.21	0.2488	0.2542	RANDOM	48.6741

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]
3.66			-1.59		-2.07

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	40.506
r_dihedral_angle_4_deg	18.003
r_dihedral_angle_3_deg	17.109
r_dihedral_angle_1_deg	7.095
r_mcangle_it	4.853
r_mcbond_other	3.204
r_mcbond_it	3.203
r_angle_refined_deg	1.564
r_angle_other_deg	0.805
r_chiral_restr	0.094
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3338
Nucleic Acid Atoms
Solvent Atoms	94
Heterogen Atoms	38

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
Macromolecular	data collection
HKL-2000	data reduction