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Crystal structure of anti-osteopontin antibody 23C3 in complex with W43A mutated epitope peptide
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 (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 3CXD 2.8 20 11543 11476 609 99.42 0.24378 0.24088 0.2413 0.29729 0.2418 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
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