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Crystal structure of anti-osteopontin antibody 23C3 in complex with its epitope peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1JHK PDB ENTRY 1JHK
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.2 277 0.2M di-sodium tartrate, 20% PEG3350, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.51 50.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.318 α = 90 b = 92.02 β = 90 c = 122.483 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++ 2008-03-08 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 98.4 0.135 5 6.65 12125
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 2.8 2.9 100 0.293 2.1 7.04 1194
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation 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) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1JHK 2.8 20 12083 613 98.1 0.251 0.248 0.2473 0.292 0.2496 RANDOM 35.378
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] 2.7 -1.43 -1.27
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.11 r_dihedral_angle_3_deg 16.798 r_dihedral_angle_4_deg 13.544 r_dihedral_angle_1_deg 4.925 r_scangle_it 1.652 r_rigid_bond_restr 1.51 r_scbond_it 1.32 r_mcangle_it 1.244 r_angle_refined_deg 1.003 r_mcbond_it 0.697
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.11 r_dihedral_angle_3_deg 16.798 r_dihedral_angle_4_deg 13.544 r_dihedral_angle_1_deg 4.925 r_scangle_it 1.652 r_rigid_bond_restr 1.51 r_scbond_it 1.32 r_mcangle_it 1.244 r_angle_refined_deg 1.003 r_mcbond_it 0.697 r_sphericity_bonded 0.555 r_nbtor_refined 0.302 r_nbd_refined 0.188 r_symmetry_vdw_refined 0.128 r_xyhbond_nbd_refined 0.123 r_chiral_restr 0.065 r_symmetry_hbond_refined 0.058 r_bond_refined_d 0.006 r_gen_planes_refined 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3323 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 50
Software Software Software Name Purpose d*TREK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction CrystalClear data scaling