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Complex of a camelid single-domain vhh antibody fragment with RNASE A at 2.5A resolution: SE5B-TRI crystal form with five se-met sites (L4M, M34, M51, F68M, M83) in vhh scaffold.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P45 PDB ID 2P45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 295 HAMPTON RESEARCH INDEX SCREEN, SOLUTION #68: (NH4)SO4,
PEG 3350, HEPES BUFFER, PH 7.5, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.71 54.64
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.011 α = 90 b = 72.011 β = 90 c = 98.012 γ = 120
Symmetry Space Group P 31 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 100 CCD ADSC QUANTUM 210 MIRRORS 2004-04-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 17-ID 0.97934 APS 17-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 20 96.1 4.9 10142 10142
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 ID 2P45 2.5 20 10142 9649 493 96.01 0.23295 0.23295 0.22998 0.2343 0.29438 0.3015 RANDOM 84.208
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] 4.76 2.38 4.76 -7.14
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.271 r_dihedral_angle_3_deg 16.271 r_dihedral_angle_4_deg 10.048 r_dihedral_angle_1_deg 7.452 r_angle_refined_deg 1.216 r_angle_other_deg 0.745 r_symmetry_vdw_refined 0.216 r_nbd_refined 0.215 r_symmetry_vdw_other 0.208 r_nbd_other 0.188
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.271 r_dihedral_angle_3_deg 16.271 r_dihedral_angle_4_deg 10.048 r_dihedral_angle_1_deg 7.452 r_angle_refined_deg 1.216 r_angle_other_deg 0.745 r_symmetry_vdw_refined 0.216 r_nbd_refined 0.215 r_symmetry_vdw_other 0.208 r_nbd_other 0.188 r_xyhbond_nbd_refined 0.17 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_other 0.128 r_nbtor_other 0.08 r_chiral_restr 0.065 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_refined r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_scbond_it r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1844 Nucleic Acid Atoms Solvent Atoms 19 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing