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Structure of HIV Protease NL4-3 in an Unliganded State
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 281.16 100mM Tris HCl, 0.2M MgCl2, 15% PEG 8K, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281.16K
Crystal Properties Matthews coefficient Solvent content 2.92 57.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.985 α = 90 b = 48.985 β = 90 c = 105.62 γ = 90
Symmetry Space Group P 41 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 RIGAKU SATURN 92 Rigaku VariMax HF Confocal Mirror 2006-05-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU
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 2.15 44.44 99.7 0.095 8.9 7.34 13572 13526 2 3
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 2.15 2.23 99.5 0.601 2.2 7.24 1334
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 MOLECULAR REPLACEMENT THROUGHOUT 2.15 44.46 7074 393 99.57 0.23834 0.23409 0.218 0.32073 0.2965 RANDOM 38.072
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] 0.8 0.8 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.988 r_dihedral_angle_4_deg 17.376 r_dihedral_angle_3_deg 17.117 r_dihedral_angle_1_deg 10.26 r_scangle_it 7.613 r_scbond_it 5.677 r_mcangle_it 3.539 r_mcbond_it 2.54 r_angle_refined_deg 2.034 r_symmetry_vdw_refined 0.327
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.988 r_dihedral_angle_4_deg 17.376 r_dihedral_angle_3_deg 17.117 r_dihedral_angle_1_deg 10.26 r_scangle_it 7.613 r_scbond_it 5.677 r_mcangle_it 3.539 r_mcbond_it 2.54 r_angle_refined_deg 2.034 r_symmetry_vdw_refined 0.327 r_nbtor_refined 0.313 r_nbd_refined 0.235 r_xyhbond_nbd_refined 0.211 r_symmetry_hbond_refined 0.191 r_chiral_restr 0.168 r_bond_refined_d 0.023 r_gen_planes_refined 0.008 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 760 Nucleic Acid Atoms Solvent Atoms 41 Heterogen Atoms 16
Software Software Software Name Purpose REFMAC refinement MOLREP phasing CNS refinement PDB_EXTRACT data extraction CrystalClear data reduction d*TREK data scaling