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Structure of the HIV-1 gp41 Membrane-Proximal Ectodomain Region in a Putative Prefusion Conformation
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GCM PDB ENTRY 1GCM
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.6 298 0.1M sodium HEPES, 0.1M ammonium dihydrogenphosphate, 50% MPD, pH 7.6, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
Crystal Properties Matthews coefficient Solvent content 2.57 52.06
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 42.527 α = 90 b = 48.157 β = 95.38 c = 81.782 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 4 2003-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.9791 NSLS X4A
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 2 19.6 98 0.049 14.1 3.7 22010 22010 39.2
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) 2 2.07 97.5 0.528 2.3 3.6 2171
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1GCM 2 19.55 22010 22010 1110 98 0.21636 0.21636 0.21347 0.2152 0.26908 0.2731 RANDOM 57.436
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] 0.93 -0.58 2.96 -4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.858 r_dihedral_angle_3_deg 18.903 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_1_deg 4.795 r_scangle_it 4.446 r_scbond_it 3.441 r_mcangle_it 2.125 r_angle_refined_deg 2.029 r_mcbond_it 1.384 r_nbtor_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.858 r_dihedral_angle_3_deg 18.903 r_dihedral_angle_4_deg 18.19 r_dihedral_angle_1_deg 4.795 r_scangle_it 4.446 r_scbond_it 3.441 r_mcangle_it 2.125 r_angle_refined_deg 2.029 r_mcbond_it 1.384 r_nbtor_refined 0.327 r_symmetry_hbond_refined 0.289 r_symmetry_vdw_refined 0.287 r_nbd_refined 0.237 r_xyhbond_nbd_refined 0.192 r_chiral_restr 0.139 r_bond_refined_d 0.026 r_gen_planes_refined 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2241 Nucleic Acid Atoms Solvent Atoms 142 Heterogen Atoms 25
Software Software Software Name Purpose ADSC data collection AMoRE phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling