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Crystal structure of murine reference antibody 125-2H Fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FNS PDB ENTRY 1FNS
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 277 FAB (13 MG/ML, 2 MICROLITERS [UL]) WAS MIXED WITH 2 UL OF RESERVOIR (10% POLYETHYLENEGLYCOL (PEG) 6000, 100 MM HEPES, PH 7.5, 5% 2, 4-METHYLPENTANEDIOL) AND SUSPENDED OVER THE RESERVOIR AT 277 K. ROD-LIKE CRYSTALS APPEARED WITHIN ONE DAY.
Crystal Properties Matthews coefficient Solvent content 2.7 54.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.061 α = 90 b = 92.49 β = 90 c = 137.645 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 CCD MARRESEARCH MIRROR 2003-03-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID APS 17-ID
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 2.33 17.5 94 0.05 18.9 5.2 41229 2 41
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 2.33 2.39 25.2 0.24 4.9 2.4
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 1FNS 2.36 17.42 39136 2091 98.2 0.187 0.184 0.1889 0.242 0.243 RANDOM 49.19
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] 0.18 0.06 -0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.931 r_dihedral_angle_4_deg 16.083 r_dihedral_angle_3_deg 14.303 r_dihedral_angle_1_deg 6.491 r_scangle_it 2.189 r_angle_refined_deg 1.501 r_scbond_it 1.416 r_mcangle_it 0.906 r_mcbond_it 0.551 r_nbtor_refined 0.297
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.931 r_dihedral_angle_4_deg 16.083 r_dihedral_angle_3_deg 14.303 r_dihedral_angle_1_deg 6.491 r_scangle_it 2.189 r_angle_refined_deg 1.501 r_scbond_it 1.416 r_mcangle_it 0.906 r_mcbond_it 0.551 r_nbtor_refined 0.297 r_symmetry_vdw_refined 0.21 r_symmetry_hbond_refined 0.19 r_nbd_refined 0.188 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6588 Nucleic Acid Atoms Solvent Atoms 488 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing