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Crystal structure of the Fab M75
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NBV pdb entry 1NBV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 291 15% PEG 4000, 100 mM Tris, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.11 41.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.982 α = 85.3 b = 43.154 β = 88.45 c = 57.37 γ = 84.29
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 150 IMAGE PLATE MAR scanner 345 mm plate 2001-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591
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 2.1 30 90.7 0.069 0.069 6.5 57110 57110 39.4
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 2.1 2.18 68.6 0.304 0.304 1573
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 1NBV 2.1 20.46 15795 15795 1417 75.84 0.22394 0.21934 0.2093 0.27292 0.2625 RANDOM 31.073
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] -0.68 -0.52 0.2 0.28 -0.22 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.362 r_dihedral_angle_4_deg 23.045 r_dihedral_angle_3_deg 19.838 r_dihedral_angle_1_deg 10.356 r_scangle_it 2.001 r_angle_refined_deg 1.547 r_scbond_it 1.328 r_mcangle_it 0.861 r_mcbond_it 0.497 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.362 r_dihedral_angle_4_deg 23.045 r_dihedral_angle_3_deg 19.838 r_dihedral_angle_1_deg 10.356 r_scangle_it 2.001 r_angle_refined_deg 1.547 r_scbond_it 1.328 r_mcangle_it 0.861 r_mcbond_it 0.497 r_nbtor_refined 0.304 r_nbd_refined 0.236 r_symmetry_hbond_refined 0.215 r_symmetry_vdw_refined 0.204 r_xyhbond_nbd_refined 0.173 r_chiral_restr 0.101 r_bond_refined_d 0.011 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3276 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement MAR345 data collection DENZO data reduction SCALEPACK data scaling EPMR phasing