3DSF

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


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3CXDPDB ENTRY 3CXD

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.92770.2M di-ammonium hydrogen phosphate, 20% PEG3350, pH 7.9, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.4750.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 41.73α = 90
b = 92.058β = 90
c = 122.104γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2008-07-01MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.5418

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.82099.40.0841215912086
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)RedundancyNumber Unique Reflections (All)
12.82.999.40.2290.2293.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 3CXD2.820115431147660999.420.243780.240880.29729RANDOM33.454
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]
0.740.5-1.24
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.946
r_dihedral_angle_3_deg19.117
r_dihedral_angle_4_deg15.178
r_dihedral_angle_1_deg5.537
r_rigid_bond_restr2.026
r_scangle_it1.884
r_scbond_it1.87
r_angle_refined_deg1.171
r_mcangle_it1.077
r_sphericity_bonded0.924
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.946
r_dihedral_angle_3_deg19.117
r_dihedral_angle_4_deg15.178
r_dihedral_angle_1_deg5.537
r_rigid_bond_restr2.026
r_scangle_it1.884
r_scbond_it1.87
r_angle_refined_deg1.171
r_mcangle_it1.077
r_sphericity_bonded0.924
r_mcbond_it0.603
r_nbtor_refined0.307
r_symmetry_hbond_refined0.202
r_nbd_refined0.198
r_symmetry_vdw_refined0.176
r_xyhbond_nbd_refined0.127
r_chiral_restr0.099
r_bond_refined_d0.01
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3302
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
CrystalCleardata collection
CrystalCleardata reduction
CrystalCleardata scaling
PHASERphasing