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Structure of the 1121B Fab fragment
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1YY9 PDB ENTRY 1YY9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 298 100 mM Na/K phosphate, pH 5.5, 40% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.79 55.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.426 α = 90 b = 66.426 β = 90 c = 203.868 γ = 120
Symmetry Space Group P 32 2 1
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 RIGAKU SATURN 944 2008-01-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.54
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.2 70 97.5 0.06 20.5 7 27477 26790 -3
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 2.2 2.28 78.7 0.219 4.5 3.3
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 1YY9 2.2 50.1 27461 25334 1345 97.15 0.1852 0.18313 0.1899 0.22311 0.2231 RANDOM 36.381
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] 0.43 0.22 0.43 -0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.701 r_dihedral_angle_4_deg 22.116 r_dihedral_angle_3_deg 15.06 r_dihedral_angle_1_deg 7.06 r_scangle_it 2.152 r_scbond_it 1.561 r_angle_refined_deg 1.372 r_mcangle_it 0.92 r_angle_other_deg 0.871 r_mcbond_it 0.727
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.701 r_dihedral_angle_4_deg 22.116 r_dihedral_angle_3_deg 15.06 r_dihedral_angle_1_deg 7.06 r_scangle_it 2.152 r_scbond_it 1.561 r_angle_refined_deg 1.372 r_mcangle_it 0.92 r_angle_other_deg 0.871 r_mcbond_it 0.727 r_symmetry_vdw_other 0.214 r_symmetry_hbond_refined 0.208 r_nbd_other 0.199 r_nbd_refined 0.189 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.172 r_symmetry_vdw_refined 0.143 r_mcbond_other 0.127 r_nbtor_other 0.084 r_chiral_restr 0.08 r_bond_refined_d 0.012 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3223 Nucleic Acid Atoms Solvent Atoms 278 Heterogen Atoms 5
Software Software Software Name Purpose CrystalClear data collection PHASER phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling