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Crystal structure of the Fab fragment of anti-osteocalcin C-terminal peptide antibody KTM219
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4KUZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 293 0.6 M sodium formate, 29% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.18 43.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.8 α = 90 b = 71.472 β = 90 c = 96.882 γ = 90
Symmetry Space Group P 21 2 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 315r 2014-11-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 1.0000 Photon Factory BL-5A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.9 50 98.8 0.066 0.071 0.027 12.5 6.8 35733 25.3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 97.5 0.484 0.522 0.194 0.918 4.23 6.8
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 4KUZ 1.9 50 33891 1786 98.62 0.1828 0.1806 0.1889 0.2235 0.2323 RANDOM 31.038
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] -0.95 0.3 0.66
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.011 r_dihedral_angle_4_deg 17.487 r_dihedral_angle_3_deg 13.377 r_dihedral_angle_1_deg 6.779 r_angle_refined_deg 1.539 r_angle_other_deg 0.914 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_bond_other_d 0.006 r_gen_planes_refined 0.006
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.011 r_dihedral_angle_4_deg 17.487 r_dihedral_angle_3_deg 13.377 r_dihedral_angle_1_deg 6.779 r_angle_refined_deg 1.539 r_angle_other_deg 0.914 r_chiral_restr 0.082 r_bond_refined_d 0.011 r_bond_other_d 0.006 r_gen_planes_refined 0.006 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3271 Nucleic Acid Atoms Solvent Atoms 239 Heterogen Atoms 83
Software Software Software Name Purpose DENZO data reduction HKL-2000 data scaling PHASER phasing Coot model building REFMAC refinement PDB_EXTRACT data extraction SCALEPACK data scaling