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X-ray structure of a camelid affinity matured single-domain vhh antibody fragment in complex with RNASE A
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2P49 PDB entry 2P49
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 5.5 295 HAMPTON RESEARCH INDEX SCREEN, SOLUTION #67, pH 5.5, VAPOR DIFFUSION, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.98 58.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.027 α = 90 b = 131.623 β = 90 c = 137.156 γ = 90
Symmetry Space Group C 2 2 21
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 MARMOSAIC 300 mm CCD 2006-04-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.0 APS 23-ID-D
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 1.9 20 99.1 7.1 48836 48836
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2P49 1.9 20 48836 46352 2484 97.96 0.18587 0.18587 0.18417 0.21807 0.2792 RANDOM 27.164
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] 2.25 -1.55 -0.71
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.252 r_dihedral_angle_4_deg 12.246 r_dihedral_angle_3_deg 11.704 r_dihedral_angle_1_deg 5.939 r_scangle_it 2.103 r_scbond_it 1.511 r_angle_refined_deg 1.335 r_mcangle_it 0.917 r_mcbond_it 0.812 r_angle_other_deg 0.735
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.252 r_dihedral_angle_4_deg 12.246 r_dihedral_angle_3_deg 11.704 r_dihedral_angle_1_deg 5.939 r_scangle_it 2.103 r_scbond_it 1.511 r_angle_refined_deg 1.335 r_mcangle_it 0.917 r_mcbond_it 0.812 r_angle_other_deg 0.735 r_symmetry_hbond_refined 0.257 r_nbd_refined 0.194 r_nbd_other 0.192 r_symmetry_vdw_other 0.184 r_symmetry_vdw_refined 0.152 r_mcbond_other 0.132 r_xyhbond_nbd_refined 0.121 r_nbtor_other 0.081 r_chiral_restr 0.06 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_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 3704 Nucleic Acid Atoms Solvent Atoms 361 Heterogen Atoms 10
Software Software Software Name Purpose REFMAC refinement HKL-3000 data collection HKL-3000 data reduction HKL-3000 data scaling MOLREP phasing