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Crystal Structure of a Murine Fab in Complex with an 11 Residue Peptide Derived from Staphylococcal Nuclease
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1F11 PDB entries: 1f11, 2aju, 1f58, 1cr9 experimental model PDB 2AJU PDB entries: 1f11, 2aju, 1f58, 1cr9 experimental model PDB 1F58 PDB entries: 1f11, 2aju, 1f58, 1cr9 experimental model PDB 1CR9 PDB entries: 1f11, 2aju, 1f58, 1cr9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 291 18% PEG 2000, 16% isopropanol, 0.1 M sodium citrate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.59 52.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.739 α = 90 b = 131.04 β = 90 c = 291.34 γ = 90
Symmetry Space Group C 2 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 100 CCD ADSC QUANTUM 315 Pt coated toroidal Si mirror 2004-10-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X25 1.1000 NSLS X25
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 2.8 50 84.6 0.12 0.12 24.1 4.4 42035 42035 -3
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.8 2.9 83.6 0.489 0.489 4.9 4.8
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-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entries: 1f11, 2aju, 1f58, 1cr9 2.81 48.74 41984 39809 2175 84.25 0.22451 0.22074 0.29278 RANDOM 37.415
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] 0.24 -0.45 0.21
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.303 r_dihedral_angle_3_deg 20.904 r_dihedral_angle_4_deg 20.022 r_dihedral_angle_1_deg 8.095 r_scangle_it 2.641 r_scbond_it 1.616 r_angle_refined_deg 1.394 r_mcangle_it 1.136 r_mcbond_it 0.646 r_symmetry_vdw_refined 0.338
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.303 r_dihedral_angle_3_deg 20.904 r_dihedral_angle_4_deg 20.022 r_dihedral_angle_1_deg 8.095 r_scangle_it 2.641 r_scbond_it 1.616 r_angle_refined_deg 1.394 r_mcangle_it 1.136 r_mcbond_it 0.646 r_symmetry_vdw_refined 0.338 r_nbtor_refined 0.317 r_symmetry_hbond_refined 0.259 r_nbd_refined 0.257 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.096 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13309 Nucleic Acid Atoms Solvent Atoms 62 Heterogen Atoms 7
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling AMoRE phasing