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HIV-1 PR mutant in complex with nelfinavir
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1NH0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 298 reservoir solution: 0.5M (NH4)2SO4, 0.1M MES pH 5.4 or pH 5.5; drops: 2+1ul (protein+reservoir}; protein: 3-5mg/ml 5-fold molar excess of inhibitor, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.15 42.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.5 α = 90 b = 62.5 β = 90 c = 82.06 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 120 IMAGE PLATE MAR scanner 345 mm plate 2005-03-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE ENRAF-NONIUS FR591 1.54179
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.2 54.23 95.93 0.079 0.079 6.7 7.1 8471 8471 32.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.32 87.8 0.377 0.377 1.9 6.5 1177
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 1NH0 2.2 54.23 8471 430 95.93 0.20491 0.2033 0.2106 0.23603 0.2369 RANDOM 26.877
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] 0.27 0.13 0.27 -0.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.495 r_dihedral_angle_3_deg 14.782 r_dihedral_angle_4_deg 14.464 r_dihedral_angle_1_deg 6.964 r_scangle_it 2.593 r_scbond_it 1.787 r_angle_refined_deg 1.578 r_mcangle_it 1.131 r_mcbond_it 0.667 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.495 r_dihedral_angle_3_deg 14.782 r_dihedral_angle_4_deg 14.464 r_dihedral_angle_1_deg 6.964 r_scangle_it 2.593 r_scbond_it 1.787 r_angle_refined_deg 1.578 r_mcangle_it 1.131 r_mcbond_it 0.667 r_nbtor_refined 0.312 r_symmetry_vdw_refined 0.219 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.197 r_symmetry_hbond_refined 0.167 r_chiral_restr 0.094 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 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 1516 Nucleic Acid Atoms Solvent Atoms 100 Heterogen Atoms 80
Software Software Software Name Purpose MAR345dtb data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling