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Crystal structure of a thermostable serine protease AL20 from extremophilic microoganism
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P3E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.9 294 2.9M sodium formate, 0.1M sodium citrate, pH 6.9, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.46 50.02
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 92.26 α = 90 b = 92.26 β = 90 c = 137.88 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 100 CCD MAR CCD 130 mm mirror 2002-01-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON MAX II BEAMLINE I711 1.076 MAX II I711
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 1.39 19.8 98 0.049 0.047 14.5 3.3 88125 86325 18.16
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) 1.39 1.44 89.4 0.193 0.193 3.5 3 8921
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 MOLECULAR REPLACEMENT THROUGHOUT 1P3E 1.39 19.18 86325 84142 2161 97.5 0.17887 0.17887 0.17834 0.1776 0.19904 0.1979 RANDOM 14.788
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 33.033 r_dihedral_angle_3_deg 12.091 r_dihedral_angle_4_deg 8.435 r_dihedral_angle_1_deg 7.286 r_scangle_it 2.183 r_scbond_it 1.49 r_angle_refined_deg 1.314 r_mcangle_it 1.068 r_mcbond_it 0.616 r_nbtor_refined 0.308
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.033 r_dihedral_angle_3_deg 12.091 r_dihedral_angle_4_deg 8.435 r_dihedral_angle_1_deg 7.286 r_scangle_it 2.183 r_scbond_it 1.49 r_angle_refined_deg 1.314 r_mcangle_it 1.068 r_mcbond_it 0.616 r_nbtor_refined 0.308 r_nbd_refined 0.215 r_symmetry_vdw_refined 0.175 r_chiral_restr 0.174 r_xyhbond_nbd_refined 0.129 r_symmetry_hbond_refined 0.126 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 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 3208 Nucleic Acid Atoms Solvent Atoms 663 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MAR345dtb data collection XDS data reduction XSCALE data scaling MOLREP phasing