3TPK | pdb_00003tpk

Crystal structure of the oligomer-specific KW1 antibody fragment

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3LN9	PDB entry 3LN9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	288	200 mM Magnesium Formate, 20%(w/v)PEG 3350, Additive: Benzamidine Hydrochloride 1M , pH 5.9, VAPOR DIFFUSION, HANGING DROP, temperature 288K

Crystal Properties
Matthews coefficient	Solvent content
1.87	34.16

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 30.921	α = 90
b = 38.659	β = 90
c = 94.412	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 225 mm CCD		2011-05-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.1	0.9184	BESSY	14.1

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	1.21	30	89.3	0.031	19.86	3.2	35385	31606	2	-3	16.062

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	1.21	1.24	46.8		0.383	1.85

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 3LN9	1.3	25.87	31606	27804	1391	100	0.143	0.143	0.1412	0.14	0.1761	0.17	RANDOM	15.3404

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]
0.23			-0.03		-0.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.513
r_dihedral_angle_4_deg	14.893
r_sphericity_free	13.191
r_dihedral_angle_3_deg	12.221
r_sphericity_bonded	8.294
r_dihedral_angle_1_deg	6.522
r_scangle_it	6.44
r_scbond_it	4.718
r_mcangle_it	3.944
r_rigid_bond_restr	2.794
r_mcbond_it	2.73
r_angle_refined_deg	2.046
r_chiral_restr	0.147
r_bond_refined_d	0.026
r_gen_planes_refined	0.013

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	934
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	13

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345dtb	data collection
XDS	data reduction