☰ Navigation Tabs
Crystal structure of carbon-sulfur lyase involved in aluminum resistance (YP_878183.1) from CLOSTRIDIUM NOVYI NT at 2.90 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3FD0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.6 277 0.2000M (NH4)2Tartrate, 20.0000% PEG-3350, No Buffer pH 6.6, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K, VAPOR DIFFUSION, SITTING DROP
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 78.74 α = 90 b = 108.948 β = 90 c = 207.642 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 100 CCD MARMOSAIC 325 mm CCD Flat collimating mirror, toroid focusing mirror 2008-08-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 SSRL BL9-2
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 2.9 29.775 99.9 0.243 0.243 3.121 3.7 40426 42.549
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 2.9 2.98 100 0.749 0.749 1 3.7 2934
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MR THROUGHOUT 3FD0 2.9 29.775 40367 2022 99.86 0.225 0.223 0.2284 0.271 0.2721 RANDOM 24.943
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] -1.65 -0.4 2.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.6 r_dihedral_angle_3_deg 9.036 r_dihedral_angle_4_deg 8.808 r_dihedral_angle_1_deg 2.167 r_angle_refined_deg 1.065 r_angle_other_deg 0.879 r_mcangle_it 0.526 r_scangle_it 0.397 r_mcbond_it 0.318 r_scbond_it 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.6 r_dihedral_angle_3_deg 9.036 r_dihedral_angle_4_deg 8.808 r_dihedral_angle_1_deg 2.167 r_angle_refined_deg 1.065 r_angle_other_deg 0.879 r_mcangle_it 0.526 r_scangle_it 0.397 r_mcbond_it 0.318 r_scbond_it 0.26 r_symmetry_hbond_refined 0.17 r_nbtor_refined 0.164 r_nbd_refined 0.161 r_xyhbond_nbd_refined 0.157 r_nbd_other 0.139 r_symmetry_vdw_other 0.123 r_nbtor_other 0.084 r_symmetry_vdw_refined 0.079 r_chiral_restr 0.065 r_mcbond_other 0.061 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_xyhbond_nbd_other 0.004 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 12883 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PHENIX refinement PHASER phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction