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Crystal structure analysis of anti-HIV-1 V3 Fab 2219 in complex with MN peptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7FAB pdb entry 7FAB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 298 40% PEG 400, 0.2M potassium acetate, VAPOR DIFFUSION, SITTING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.5 51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 60.471 α = 90 b = 60.471 β = 90 c = 275.194 γ = 90
Symmetry Space Group P 41 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 315 2002-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 1.033 SSRL BL9-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 69.01 99.8 0.086 22 5.3 23835 23835 -3 30.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 100 0.525 3.5 5.5 1162
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 7FAB 2.3 69.01 22624 22624 1195 99.81 0.21926 0.21926 0.21685 0.26665 0.2469 RANDOM 31.648
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] 0.95 0.95 -1.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.716 r_dihedral_angle_3_deg 13.882 r_dihedral_angle_4_deg 12.049 r_dihedral_angle_1_deg 7.231 r_scangle_it 2.133 r_scbond_it 1.494 r_angle_refined_deg 1.458 r_mcangle_it 0.937 r_angle_other_deg 0.92 r_mcbond_it 0.751
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.716 r_dihedral_angle_3_deg 13.882 r_dihedral_angle_4_deg 12.049 r_dihedral_angle_1_deg 7.231 r_scangle_it 2.133 r_scbond_it 1.494 r_angle_refined_deg 1.458 r_mcangle_it 0.937 r_angle_other_deg 0.92 r_mcbond_it 0.751 r_symmetry_vdw_other 0.241 r_nbd_refined 0.206 r_nbd_other 0.189 r_nbtor_refined 0.177 r_symmetry_hbond_refined 0.169 r_xyhbond_nbd_refined 0.162 r_symmetry_vdw_refined 0.144 r_chiral_restr 0.13 r_mcbond_other 0.127 r_nbtor_other 0.085 r_bond_refined_d 0.013 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3449 Nucleic Acid Atoms Solvent Atoms 191 Heterogen Atoms 20
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing CNS refinement DENZO data reduction