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Structure of DC8E8 Fab crystallized at pH 8.5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 295 30% PEG 4000, 0.1 M Tris, 0.2 M MgCl2
Crystal Properties Matthews coefficient Solvent content 2.29 46.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.11 α = 90 b = 111.03 β = 90.38 c = 95.86 γ = 90
Symmetry Space Group P 1 21 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 MARMOSAIC 225 mm CCD 2008-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06DA 1.0000 SLS X06DA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) 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 2.98 37.87 83.2 0.121 0.154 0.987 8.26 2.376 14700 -3 48.032
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.98 3.06 85.5 0.511 0.653 0.776 1.94 2.276
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4OZ4 2.98 37.87 13690 703 81.51 0.2203 0.2186 0.2559 0.2891 RANDOM 59.906
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] 61.29 -5.16 -26.53 -34.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.566 r_dihedral_angle_3_deg 15.272 r_dihedral_angle_4_deg 14.119 r_dihedral_angle_1_deg 6.792 r_angle_refined_deg 1.478 r_angle_other_deg 1.032 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.566 r_dihedral_angle_3_deg 15.272 r_dihedral_angle_4_deg 14.119 r_dihedral_angle_1_deg 6.792 r_angle_refined_deg 1.478 r_angle_other_deg 1.032 r_chiral_restr 0.077 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6680 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose XDS data reduction XSCALE data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction