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HIV gp140 trimer MD39-10MUTA in complex with Fabs PGT124 and 35022
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5CEZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.1 277 5% Peg6000
0.1M citric acid
Crystal Properties Matthews coefficient Solvent content 4.39 71.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 127.915 α = 90 b = 127.915 β = 90 c = 313.887 γ = 120
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 2016-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 1.03322 APS 23-ID-D
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 4.5 50.01 98.4 0.213 0.76 4.75 4.3 17067 -3 106
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 4.5 4.58 98.9 1 0.63 1.1 4.4
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 5CEZ 4.5 50.01 16142 844 98.43 0.27158 0.26952 0.2713 0.30877 0.3026 RANDOM 187.769
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] 2.82 1.41 2.82 -9.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.34 r_long_range_B_refined 24.369 r_long_range_B_other 24.368 r_dihedral_angle_3_deg 14.84 r_mcangle_it 12.553 r_mcangle_other 12.553 r_dihedral_angle_4_deg 12.498 r_scangle_other 11.153 r_mcbond_it 7.262 r_mcbond_other 7.256
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.34 r_long_range_B_refined 24.369 r_long_range_B_other 24.368 r_dihedral_angle_3_deg 14.84 r_mcangle_it 12.553 r_mcangle_other 12.553 r_dihedral_angle_4_deg 12.498 r_scangle_other 11.153 r_mcbond_it 7.262 r_mcbond_other 7.256 r_dihedral_angle_1_deg 6.54 r_scbond_it 6.181 r_scbond_other 6.181 r_angle_refined_deg 1.513 r_angle_other_deg 1.095 r_chiral_restr 0.09 r_bond_refined_d 0.011 r_bond_other_d 0.008 r_gen_planes_refined 0.008 r_gen_planes_other 0.002 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 11183 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 653
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling PHASER phasing