☰ Navigation Tabs
Crystal structure of Sco3058 with bound inhibitor L-Ala-L-Asp Phosphinodipeptide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3ITC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 0.2 M magnesium chloride hexahydrate, 0.1 Tris pH 8.5, 18% PEG-4000, VAPOR DIFFUSION, HANGING DROP
Crystal Properties Matthews coefficient Solvent content 3.26 62.26
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.69 α = 90 b = 96.69 β = 90 c = 104.6 γ = 120
Symmetry Space Group P 31 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray CCD ADSC QUANTUM 315r 2009-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 0.9756 SSRL BL7-1
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 2.2 83.62 99.4 29044 2 2
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 (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 3ITC 2.2 83.62 2 29175 27539 1476 99.44 0.22 0.17791 0.17521 0.174 0.22855 0.2245 RANDOM 24.974
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] -2.21 -1.11 -2.21 3.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.352 r_dihedral_angle_4_deg 16.853 r_dihedral_angle_3_deg 13.144 r_dihedral_angle_1_deg 6.869 r_scangle_it 3.927 r_scbond_it 2.682 r_angle_refined_deg 1.725 r_mcangle_it 1.442 r_mcbond_it 0.923 r_nbtor_refined 0.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.352 r_dihedral_angle_4_deg 16.853 r_dihedral_angle_3_deg 13.144 r_dihedral_angle_1_deg 6.869 r_scangle_it 3.927 r_scbond_it 2.682 r_angle_refined_deg 1.725 r_mcangle_it 1.442 r_mcbond_it 0.923 r_nbtor_refined 0.29 r_nbd_refined 0.194 r_symmetry_vdw_refined 0.187 r_symmetry_hbond_refined 0.177 r_xyhbond_nbd_refined 0.168 r_metal_ion_refined 0.135 r_chiral_restr 0.122 r_bond_refined_d 0.021 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2983 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 17
Software Software Software Name Purpose Blu-Ice data collection PHASES phasing REFMAC refinement MOSFLM data reduction SCALA data scaling