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Structure of SMUL_1544, a decarboxylase from Sulfurospirillum multivorans
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LC8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 100 mM Bis-(2-Hydroxyethyl) Amino-Tris(Hydroxymethyl) Methane (BIS-TRIS) (pH 6.0), 16% Poly(ethylene glycol) methyl ether 2,000 (MEPEG 2K), and 200 mM potassium glutamate
Crystal Properties Matthews coefficient Solvent content 2.37 48.03
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 141.53 α = 90 b = 90.627 β = 109.96 c = 70.867 γ = 90
Symmetry Space Group C 1 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 100 CCD ADSC QUANTUM 210r 2017-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-BM 0.979 APS 19-BM
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 1.94 50 99.5 0.074 16.1 4 55968
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 1.94 1.97 99.4 0.55 3.2
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 1LC8 1.94 74.9 55968 2932 94.26 0.19299 0.19003 0.1975 0.25026 0.2548 RANDOM 25.094
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] 0.01 -0.02 0.03 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.954 r_dihedral_angle_4_deg 17.016 r_dihedral_angle_3_deg 15.858 r_long_range_B_refined 7.3 r_long_range_B_other 7.063 r_dihedral_angle_1_deg 6.764 r_scangle_other 4.814 r_mcangle_it 3.354 r_mcangle_other 3.353 r_scbond_it 3.089
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.954 r_dihedral_angle_4_deg 17.016 r_dihedral_angle_3_deg 15.858 r_long_range_B_refined 7.3 r_long_range_B_other 7.063 r_dihedral_angle_1_deg 6.764 r_scangle_other 4.814 r_mcangle_it 3.354 r_mcangle_other 3.353 r_scbond_it 3.089 r_scbond_other 3.088 r_mcbond_it 2.282 r_mcbond_other 2.282 r_angle_refined_deg 1.953 r_angle_other_deg 0.944 r_chiral_restr 0.115 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.006 r_gen_planes_other 0.001 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6029 Nucleic Acid Atoms Solvent Atoms 499 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling HKL-3000 phasing