☰ Navigation Tabs
Crystal structure of the HIV-1 gp41 MPER-specific llama VHH 2H10
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EZJ PDB ENTRY 3EZJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 9 0.1 M BICINE, 3.2 M (NH4)2SO4, PH 9
Crystal Properties Matthews coefficient Solvent content 2.21 44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 89.95 α = 90 b = 89.95 β = 90 c = 89.95 γ = 90
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 CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge 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 1.3 25 99 0.07 6.1 13.9 28043 2.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.3 1.37 100 0.3 2.2 14.2
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) 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 3EZJ 1.3 63.6 28043 1499 98.94 0.1468 0.14502 0.1432 0.17963 0.1772 RANDOM 20.105
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.444 r_rigid_bond_restr 29.368 r_sphericity_bonded 17.611 r_dihedral_angle_4_deg 14.196 r_dihedral_angle_3_deg 12.327 r_dihedral_angle_1_deg 5.927 r_angle_refined_deg 1.16 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.444 r_rigid_bond_restr 29.368 r_sphericity_bonded 17.611 r_dihedral_angle_4_deg 14.196 r_dihedral_angle_3_deg 12.327 r_dihedral_angle_1_deg 5.927 r_angle_refined_deg 1.16 r_chiral_restr 0.075 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_sphericity_free
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 935 Nucleic Acid Atoms Solvent Atoms 172 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing