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CRYSTAL STRUCTURE OF THE INNER DOMAIN OF CLADE A/E HIV-1 GP120 IN COMPLEX WITH THE ADCC-POTENT RHESUS MACAQUE ANTIBODY JR4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RFE
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 294 20% PEG MONOMETHYL ETHER 5000, 0.2M
AMMONIUM SULFATE, 0.1M TRIS-HCL PH 7.5, VAPOR DIFFUSION, HANGING
DROP, TEMPERATURE 294K
Crystal Properties Matthews coefficient Solvent content 2.4 48.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.447 α = 90 b = 89.848 β = 90 c = 180.783 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 PIXEL DECTRIS PILATUS 6M RH COATED FLAT MIRROR 2014-01-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 0.97950 SSRL BL12-2
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 1.85 50 94.9 0.107 15 5.8 51569
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 1.85 1.88 91.4 1 1.1 5.7
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 2RFE 1.85 50 48756 2617 94.3 0.186 0.184 0.1916 0.223 0.2283 RANDOM 44.5
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] -1.5 -0.24 1.74
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.832 r_dihedral_angle_4_deg 16.193 r_dihedral_angle_3_deg 15.555 r_dihedral_angle_1_deg 7.507 r_long_range_B_refined 6.438 r_long_range_B_other 6.306 r_scangle_other 3.833 r_mcangle_it 2.823 r_mcangle_other 2.823 r_scbond_it 2.512
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.832 r_dihedral_angle_4_deg 16.193 r_dihedral_angle_3_deg 15.555 r_dihedral_angle_1_deg 7.507 r_long_range_B_refined 6.438 r_long_range_B_other 6.306 r_scangle_other 3.833 r_mcangle_it 2.823 r_mcangle_other 2.823 r_scbond_it 2.512 r_scbond_other 2.485 r_mcbond_it 1.853 r_mcbond_other 1.851 r_angle_refined_deg 1.792 r_angle_other_deg 0.891 r_chiral_restr 0.118 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4034 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 32
Software Software Software Name Purpose HKL-2000 data reduction HKL-2000 data scaling PHASER phasing REFMAC refinement