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Structure of ligand-free Fab DNA-1 in space group P321 solved from crystals with perfect hemihedral twinning
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 4.9 298 ammonium sulfate, sodium acetate, pH 4.9, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 4.4 72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 179.179 α = 90 b = 179.179 β = 90 c = 91.985 γ = 120
Symmetry Space Group P 3 2 1
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 2.5 49.5 87 0.09 0.09 13 5.8 54454 54454
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 2.5 2.59 81 0.511 0.511 2.9
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 2.5 49.5 51454 41498 4384 77.8 0.18696 0.18696 0.18303 0.1812 0.22398 0.2181 RANDOM 23.847
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] -0.29 -0.15 -0.29 0.44
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.066 r_scangle_it 2.315 r_scbond_it 1.512 r_angle_refined_deg 1.511 r_mcangle_it 0.973 r_mcbond_it 0.53 r_symmetry_vdw_refined 0.265 r_symmetry_hbond_refined 0.238 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.147
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.066 r_scangle_it 2.315 r_scbond_it 1.512 r_angle_refined_deg 1.511 r_mcangle_it 0.973 r_mcbond_it 0.53 r_symmetry_vdw_refined 0.265 r_symmetry_hbond_refined 0.238 r_nbd_refined 0.229 r_xyhbond_nbd_refined 0.147 r_chiral_restr 0.096 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_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 6360 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 15
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing