☰ Navigation Tabs
D-Cysteine desulfhydrase from Salmonella typhimurium complexed with L-cycloserine (LCS)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4D8T PDB ENTRY 4D8T
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 298 1.5M Ammonium sulphate, 15% (v/v) ethylene glycol, 0.1M HEPES, 0.2% Benzamidine, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.24 45.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.42 α = 90 b = 165.84 β = 119.03 c = 68.06 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate mirrors 2010-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER AXS MICROSTAR 1.5418
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 2.44 59.51 87.3 0.103 8.2 3.4 41742
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) 1 2.44 2.57 58.7 0.232 4.2 3.1 4058
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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4D8T 2.47 58.08 39608 2122 90.07 0.21518 0.21262 0.2113 0.26274 0.263 RANDOM 22.176
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] 0.02 0.02 -0.03 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.611 r_dihedral_angle_4_deg 25.751 r_dihedral_angle_3_deg 15.952 r_dihedral_angle_1_deg 6.415 r_scangle_it 2.766 r_angle_refined_deg 1.94 r_scbond_it 1.64 r_mcangle_it 1.062 r_mcbond_it 0.564 r_chiral_restr 0.122
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.611 r_dihedral_angle_4_deg 25.751 r_dihedral_angle_3_deg 15.952 r_dihedral_angle_1_deg 6.415 r_scangle_it 2.766 r_angle_refined_deg 1.94 r_scbond_it 1.64 r_mcangle_it 1.062 r_mcbond_it 0.564 r_chiral_restr 0.122 r_bond_refined_d 0.017 r_gen_planes_refined 0.007 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 9664 Nucleic Acid Atoms Solvent Atoms 248 Heterogen Atoms 115
Software Software Software Name Purpose MAR345dtb data collection PHASER phasing REFMAC refinement MOSFLM data reduction SCALA data scaling