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1.3A Structure of alpha-Lytic Protease Bound to Ac-AlaAlaPro-Alanal
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2H5C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.8 277 1.2M Li2SO4, 20mM Tris-SO4, pH 4.8, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.31 46.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.936 α = 90 b = 63.936 β = 90 c = 316.897 γ = 120
Symmetry Space Group P 61 2 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 ADSC QUANTUM 4 2009-02-28 SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X26C NSLS X26C
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.3 26.1 85626
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 (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 2H5C 1.3 26.1 96017 85626 4332 89.4 0.168 0.167 0.1874 0.192 0.2149 RANDOM 18.36
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 r_dihedral_angle_2_deg 30.872 r_dihedral_angle_4_deg 21.557 r_dihedral_angle_3_deg 12.841 r_dihedral_angle_1_deg 7.077 r_scangle_it 3.525 r_angle_refined_deg 2.96 r_scbond_it 2.797 r_mcangle_it 1.984 r_mcbond_it 1.414 r_angle_other_deg 1.402
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.872 r_dihedral_angle_4_deg 21.557 r_dihedral_angle_3_deg 12.841 r_dihedral_angle_1_deg 7.077 r_scangle_it 3.525 r_angle_refined_deg 2.96 r_scbond_it 2.797 r_mcangle_it 1.984 r_mcbond_it 1.414 r_angle_other_deg 1.402 r_mcbond_other 0.637 r_chiral_restr 0.143 r_bond_refined_d 0.027 r_gen_planes_refined 0.015 r_bond_other_d 0.003 r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined 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 2832 Nucleic Acid Atoms Solvent Atoms 525 Heterogen Atoms 79
Software Software Software Name Purpose MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction