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Crystal structure of Fab fragment of anti-osteocalcin antibody KTM219 complexed with C-terminal peptide antigen
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5X5X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.4 297 0.07 M Citric acid, 0.03 M BIS-TRIS propane, 16% Polyethylene glycol 3,350, by using random Microseed Matrix Screening (rMMS) method
Crystal Properties Matthews coefficient Solvent content 1.96 37.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 43.88 α = 90 b = 67.489 β = 90 c = 138.655 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 95 CCD ADSC QUANTUM 270 2015-12-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 2.3 50 99.1 0.151 0.165 0.066 5.3 6.1 18912
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.38 99.6 0.769 0.835 0.32 0.836 2.6 6.5
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 5X5X 2.3 50 17875 984 98.85 0.20143 0.19897 0.2059 0.24781 0.2533 RANDOM 39.498
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] -3.37 1.69 1.68
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.267 r_dihedral_angle_3_deg 16.193 r_dihedral_angle_4_deg 15.208 r_dihedral_angle_1_deg 7.489 r_long_range_B_refined 7.403 r_long_range_B_other 7.401 r_scangle_other 4.656 r_mcangle_it 3.895 r_mcangle_other 3.894 r_scbond_it 2.873
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.267 r_dihedral_angle_3_deg 16.193 r_dihedral_angle_4_deg 15.208 r_dihedral_angle_1_deg 7.489 r_long_range_B_refined 7.403 r_long_range_B_other 7.401 r_scangle_other 4.656 r_mcangle_it 3.895 r_mcangle_other 3.894 r_scbond_it 2.873 r_scbond_other 2.872 r_mcbond_other 2.487 r_mcbond_it 2.486 r_angle_refined_deg 1.654 r_angle_other_deg 0.979 r_chiral_restr 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.007 r_bond_other_d 0.006 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3319 Nucleic Acid Atoms Solvent Atoms 128 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data scaling HKL-2000 data reduction PHASER phasing