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Crystal structure of chemically synthesized 203 amino acid 'covalent dimer' [L-Ala;Gly51']HIV-1 protease molecule complexed with MVT-101 reduced isostere inhibitor at 1.4 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3HAU
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 0.1 M CITRATE, 0.2 M SODIUM PHOSPHATE, 30% (V/V) AMMONIUM SULFATE, 10% (V/V) DMSO, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.11 41.71
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.695 α = 90 b = 58.074 β = 90 c = 61.593 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 110 CCD ADSC QUANTUM 315 BENT CONICAL SI-MIRROR (RH COATING); BENT GE(111) MONOCHROMATOR 2007-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90020 APS 14-BM-C
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 1.4 50 98.4 0.068 25.46 6.4 36259
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 1.4 1.45 93 0.437 2.85 4.2 3370
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 Molrep v.5 THROUGHOUT 3HAU 1.4 20 34308 1805 97.71 0.19751 0.19649 0.2034 0.21728 0.2277 RANDOM 25.362
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] 1.61 -0.63 -0.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.619 r_dihedral_angle_4_deg 16.852 r_dihedral_angle_3_deg 13.545 r_dihedral_angle_1_deg 6.595 r_scangle_it 4.104 r_scbond_it 2.726 r_mcangle_it 1.884 r_angle_refined_deg 1.731 r_mcbond_it 1.252 r_angle_other_deg 0.94
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 40.619 r_dihedral_angle_4_deg 16.852 r_dihedral_angle_3_deg 13.545 r_dihedral_angle_1_deg 6.595 r_scangle_it 4.104 r_scbond_it 2.726 r_mcangle_it 1.884 r_angle_refined_deg 1.731 r_mcbond_it 1.252 r_angle_other_deg 0.94 r_symmetry_vdw_refined 0.399 r_mcbond_other 0.334 r_symmetry_vdw_other 0.228 r_nbd_refined 0.221 r_xyhbond_nbd_refined 0.206 r_nbd_other 0.203 r_nbtor_refined 0.175 r_symmetry_hbond_refined 0.164 r_chiral_restr 0.106 r_nbtor_other 0.091 r_bond_refined_d 0.018 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1544 Nucleic Acid Atoms Solvent Atoms 137 Heterogen Atoms 54
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling