☰ Navigation Tabs
Complex of a camelid single-domain vhh antibody fragment with RNASE A at 2.3A resolution: SE5B-tetra 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 entry 2P45
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 295 HAMPTON RESEARCH INDEX SCREEN, SOLUTION #66: (NH4)2SO4,
PEG 3350, BIS-TRIS, PH 5.5, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.92 57.88
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.324 α = 90 b = 42.324 β = 90 c = 352.873 γ = 90
Symmetry Space Group P 43 21 2
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 0.97926 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 2.3 20 94.9 8.4 15006 15006
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 2P45 2.3 20 15006 13481 1525 97.08 0.24611 0.24611 0.24054 0.2378 0.29651 0.2913 RANDOM 43.852
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] 3.01 3.01 -6.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.473 r_dihedral_angle_3_deg 18.088 r_dihedral_angle_4_deg 14.25 r_dihedral_angle_1_deg 7.881 r_scangle_it 3.74 r_scbond_it 2.686 r_mcangle_it 1.595 r_mcbond_it 1.271 r_angle_refined_deg 1.079 r_angle_other_deg 0.747
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.473 r_dihedral_angle_3_deg 18.088 r_dihedral_angle_4_deg 14.25 r_dihedral_angle_1_deg 7.881 r_scangle_it 3.74 r_scbond_it 2.686 r_mcangle_it 1.595 r_mcbond_it 1.271 r_angle_refined_deg 1.079 r_angle_other_deg 0.747 r_symmetry_vdw_refined 0.228 r_mcbond_other 0.228 r_nbd_refined 0.215 r_nbd_other 0.208 r_xyhbond_nbd_refined 0.174 r_symmetry_vdw_other 0.111 r_nbtor_other 0.089 r_chiral_restr 0.07 r_bond_refined_d 0.015 r_symmetry_hbond_refined 0.008 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_nbtor_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1858 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing