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Crystal structure of DC8E8 Fab at pH 7.0 containing a Zn atom
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4OZ4 pdbid 4OZ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 295 16% PEG 3350, 0.2 M imidazol, 0.02 M ZnSO4
Crystal Properties Matthews coefficient Solvent content 2.69 54.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 113.51 α = 90 b = 113.51 β = 90 c = 69.39 γ = 120
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 MAR CCD 165 mm 2006-12-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 0.8166 EMBL/DESY, HAMBURG X11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) Rrim 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 2.616 98.3 98.5 0.05 28.47 5.8 29733
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.616 2.67 80.6 0.804 0.794 3.16 4.9 1802
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 pdbid 4OZ4 2.62 98.3 28230 1503 98.41 0.2156 0.2122 0.2156 0.2794 0.281 RANDOM 73.988
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] 1.66 0.83 1.66 -5.38
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.411 r_dihedral_angle_4_deg 20.935 r_dihedral_angle_3_deg 19.321 r_dihedral_angle_1_deg 7.081 r_angle_refined_deg 1.732 r_angle_other_deg 1.033 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.411 r_dihedral_angle_4_deg 20.935 r_dihedral_angle_3_deg 19.321 r_dihedral_angle_1_deg 7.081 r_angle_refined_deg 1.732 r_angle_other_deg 1.033 r_chiral_restr 0.091 r_bond_refined_d 0.014 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6683 Nucleic Acid Atoms Solvent Atoms 27 Heterogen Atoms 12
Software Software Software Name Purpose XSCALE data scaling XDS data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction