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Structure of ligand-free Fab DNA-1 in space group P65
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1I8M PDB ENTRY 1I8M
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 298 isopropanol, PEG 4000, sodium citrate, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.8 55
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 201.751 α = 90 b = 201.751 β = 90 c = 44.781 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 173 CCD ADSC QUANTUM 4 2001-04-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X8C 1.072 NSLS X8C
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 2.3 48.5 99.8 0.085 0.085 16 5 46702 46702
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 2.3 2.38 99.9 0.455 0.455 3.6
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 (All) 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 1I8M 2.3 48.5 46702 44367 2323 99.38 0.20963 0.20963 0.20791 0.2103 0.24259 0.2428 RANDOM 18.652
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] 0.58 0.29 0.58 -0.88
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.553 r_scangle_it 1.934 r_angle_refined_deg 1.248 r_scbond_it 1.193 r_mcangle_it 0.875 r_angle_other_deg 0.805 r_mcbond_it 0.464 r_nbd_other 0.229 r_nbd_refined 0.178 r_symmetry_vdw_other 0.177
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.553 r_scangle_it 1.934 r_angle_refined_deg 1.248 r_scbond_it 1.193 r_mcangle_it 0.875 r_angle_other_deg 0.805 r_mcbond_it 0.464 r_nbd_other 0.229 r_nbd_refined 0.178 r_symmetry_vdw_other 0.177 r_xyhbond_nbd_refined 0.162 r_symmetry_hbond_refined 0.147 r_symmetry_vdw_refined 0.131 r_nbtor_other 0.084 r_chiral_restr 0.077 r_bond_refined_d 0.013 r_bond_other_d 0.004 r_gen_planes_refined 0.004 r_gen_planes_other 0.002 r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_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 6391 Nucleic Acid Atoms Solvent Atoms 66 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing