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Structure of an unliganded and fully-glycosylated SIV gp120 envelope glycoprotein
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5 293 PROTEIN WAS CRYSTALLIZED FROM 15% PEG 6000, 100 MM SODIUM CITRATE, PH 5.0 AND 8% PEG 400 AT 20 DEGREES C.
Crystal Properties Matthews coefficient Solvent content 3.98 68.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 108.048 α = 90 b = 108.048 β = 90 c = 117.701 γ = 90
Symmetry Space Group P 43 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 CCD RH-COATED SI MIRROR 2002-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 CHESS F1
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 4 26 98 0.08 12 4.5 100402 141.1
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 4 4.09 94.3 0.82 1.3 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIRAS THROUGHOUT 4 26 5842 279 98 0.385 0.385 0.3884 0.388 0.405 RANDOM 128.8
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] 0.01 0.01 -0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.267 r_dihedral_angle_3_deg 24.209 r_dihedral_angle_4_deg 18.61 r_dihedral_angle_1_deg 8.116 r_angle_refined_deg 2.067 r_symmetry_vdw_refined 0.368 r_nbtor_refined 0.344 r_nbd_refined 0.341 r_xyhbond_nbd_refined 0.268 r_symmetry_hbond_refined 0.194
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 45.267 r_dihedral_angle_3_deg 24.209 r_dihedral_angle_4_deg 18.61 r_dihedral_angle_1_deg 8.116 r_angle_refined_deg 2.067 r_symmetry_vdw_refined 0.368 r_nbtor_refined 0.344 r_nbd_refined 0.341 r_xyhbond_nbd_refined 0.268 r_symmetry_hbond_refined 0.194 r_chiral_restr 0.112 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2471 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 615
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing SHARP phasing REFMAC refinement