3HZK | pdb_00003hzk

Crystal structure of S73-2 antibody in complex with antigen Kdo(2.4)Kdo

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1Q9R	PDB entry 1Q9R

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	298	PEG 4000, Ethylene glycol, ZnCl2, MgCl2, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.19

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 46.34	α = 90
b = 80.94	β = 90
c = 128.16	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	IMAGE PLATE	RIGAKU RAXIS	Osmic Blue	2007-11-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-002+	1.5418

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	19.86	94.9	0.061		4.73		25575

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)
	2.15	2.23	98.2		0.296	3.8	4.66	2624

Refinement

Statistics
Diffraction ID	Structure Solution 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)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	PDB entry 1Q9R	2.15	19.752	25568	1294	94.81	0.217	0.214	0.2033	0.26	0.2452	34.031

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]
-0.081			0.157		-0.075

RMS Deviations
Key	Refinement Restraint Deviation
f_dihedral_angle_d	18.01
f_angle_d	1.065
f_chiral_restr	0.074
f_bond_d	0.006
f_plane_restr	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3387
Nucleic Acid Atoms
Solvent Atoms	166
Heterogen Atoms	37

Software

Software
Software Name	Purpose
d*TREK	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction