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Crystal structure of HIV-1 protease complexed with a product of autoproteolysis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1A30 PDB ENTRY 1A30
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 279 sodium chloride 0.8-0.9M, sodium citrate 50mM, DMSO 5%, sodium acetate 5mM, EDTA 0.5mM, DTT 0.25mM, Boc-Phe-psi[(S)-CH(OH)CH2NH]Phe-Ile-Phe-NH2 270mM, protein 3mg/ml in drop, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 279K
Crystal Properties Matthews coefficient Solvent content 2.37 47.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.765 α = 90 b = 86.284 β = 90 c = 45.834 γ = 90
Symmetry Space Group P 21 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 IMAGE PLATE MARRESEARCH 2000-07-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ELETTRA BEAMLINE 5.2R 1.0 ELETTRA 5.2R
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 1.801 25 96.7 0.049 0.049 30.8 4.3 21152 21152 14
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) 1.8 1.83 92.9 0.232 0.232 7 3.8 988
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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1A30 1.8 19.1 21129 21129 1023 96.7 0.178 0.178 0.177 0.1793 0.211 0.1745 RANDOM 15.9
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]
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.2 c_scangle_it 4.57 c_scbond_it 3.03 c_mcangle_it 2.33 c_angle_deg 1.6 c_mcbond_it 1.55 c_improper_angle_d 0.92 c_bond_d 0.013 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 26.2 c_scangle_it 4.57 c_scbond_it 3.03 c_mcangle_it 2.33 c_angle_deg 1.6 c_mcbond_it 1.55 c_improper_angle_d 0.92 c_bond_d 0.013 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1567 Nucleic Acid Atoms Solvent Atoms 135 Heterogen Atoms 19
Software Software Software Name Purpose CNS refinement DENZO data reduction SCALEPACK data scaling CNS phasing