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Crystal Structure of the plant subtilisin-like protease SBT3
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.4 277 100 mM Bicine, 2.0 M NaCl, 10% (w/v) PEG 6000, 10 mM hexamminecobalt(III) chloride, pH 8.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.63 66.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 143.89 α = 90 b = 143.89 β = 90 c = 195.14 γ = 90
Symmetry Space Group P 43 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 CCD MARMOSAIC 225 mm CCD 2007-06-30 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD MARMOSAIC 225 mm CCD 2008-05-25 M SINGLE WAVELENGTH 3 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2007-08-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.5 SLS X10SA 2 SYNCHROTRON SLS BEAMLINE X10SA 1.008 SLS X10SA 3 ROTATING ANODE RIGAKU 1.541
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 1,2,3 2.5 20 99.7 0.112 12.13 7.5 135407 71081 -6 -3
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) 2.5 3 99.9 0.424 5.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MIRAS THROUGHOUT 2.5 19.99 67526 3554 100 0.25032 0.2486 0.2466 0.28262 0.2482 RANDOM 50.096
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] -1.9 -1.9 3.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.032 r_dihedral_angle_4_deg 16.168 r_dihedral_angle_3_deg 16.118 r_dihedral_angle_1_deg 5.42 r_scangle_it 2.076 r_scbond_it 1.224 r_angle_refined_deg 1.162 r_mcangle_it 0.864 r_mcbond_it 0.458 r_chiral_restr 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.032 r_dihedral_angle_4_deg 16.168 r_dihedral_angle_3_deg 16.118 r_dihedral_angle_1_deg 5.42 r_scangle_it 2.076 r_scbond_it 1.224 r_angle_refined_deg 1.162 r_mcangle_it 0.864 r_mcbond_it 0.458 r_chiral_restr 0.09 r_gen_planes_refined 0.011 r_bond_refined_d 0.01 r_bond_other_d r_angle_other_deg 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 9666 Nucleic Acid Atoms Solvent Atoms 502 Heterogen Atoms 204
Software Software Software Name Purpose XSCALE data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction