3DSF

Crystal structure of anti-osteopontin antibody 23C3 in complex with W43A mutated epitope peptide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.9	277	0.2M di-ammonium hydrogen phosphate, 20% PEG3350, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 41.73	α = 90
b = 92.058	β = 90
c = 122.104	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 IV++		2008-07-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	2.8	20	99.4	0.084			12159	12086

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.8	2.9	99.4		0.229	0.229	3.1

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 3CXD	2.8	20	11543	11476	609	99.42	0.24378	0.24088	0.29729	RANDOM	33.454

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]
0.74			0.5		-1.24

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.946
r_dihedral_angle_3_deg	19.117
r_dihedral_angle_4_deg	15.178
r_dihedral_angle_1_deg	5.537
r_rigid_bond_restr	2.026
r_scangle_it	1.884
r_scbond_it	1.87
r_angle_refined_deg	1.171
r_mcangle_it	1.077
r_sphericity_bonded	0.924
r_mcbond_it	0.603
r_nbtor_refined	0.307
r_symmetry_hbond_refined	0.202
r_nbd_refined	0.198
r_symmetry_vdw_refined	0.176
r_xyhbond_nbd_refined	0.127
r_chiral_restr	0.099
r_bond_refined_d	0.01
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3302
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	50

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
CrystalClear	data reduction
CrystalClear	data scaling
PHASER	phasing