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CRYSTAL STRUCTURE OF DECAMER NCP1 SUBSTRATE PEPTIDE IN COMPLEX WITH WILD-TYPE D25N HIV-1 PROTEASE VARIANT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MTR
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 298 SODIUM PHOSPHATE, SODIUM CITRATE, AMMONIUM SULPHATE, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.01 38.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.058 α = 90 b = 57.731 β = 90 c = 61.495 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 220 IMAGE PLATE RIGAKU RAXIS OSMIC MIRRORS 2002-10-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
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 2.1 42.26 94.1 0.092 10450 10450 -3 -3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1MTR 2.1 42.26 -3 9912 9912 493 93.93 0.20717 0.20587 0.23355 RANDOM 40.067
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 -0.34 1.34
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 9.961 r_scbond_it 7.225 r_mcangle_it 5.128 r_dihedral_angle_1_deg 4.286 r_mcbond_it 3.623 r_angle_refined_deg 1.462 r_xyhbond_nbd_refined 0.52 r_symmetry_vdw_refined 0.465 r_symmetry_hbond_refined 0.31 r_nbd_refined 0.248
RMS Deviations Key Refinement Restraint Deviation r_scangle_it 9.961 r_scbond_it 7.225 r_mcangle_it 5.128 r_dihedral_angle_1_deg 4.286 r_mcbond_it 3.623 r_angle_refined_deg 1.462 r_xyhbond_nbd_refined 0.52 r_symmetry_vdw_refined 0.465 r_symmetry_hbond_refined 0.31 r_nbd_refined 0.248 r_chiral_restr 0.178 r_gen_planes_refined 0.017 r_bond_refined_d 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1526 Nucleic Acid Atoms Solvent Atoms 112 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement SCALEPACK data scaling AMoRE phasing