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Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved in antioxidative response (TM1620) from Thermotoga maritima at 1.56 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1P8C
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 277 5.5 MES 25 MPD 0.2 Li2SO4, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.69 53.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.922 α = 90 b = 67.975 β = 97.52 c = 90.077 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 CCD ADSC 2003-10-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 5.0.1 ALS 5.0.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.56 50 92.29 0.04 32.69 3.8 106734 30.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.56 1.62 55.27 0.48 1.32 1.78 6403
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 1P8C 1.56 44.65 101346 5361 92.21 0.15918 0.15816 0.1717 0.17834 0.1886 RANDOM 15.887
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] -0.77 -0.85 -0.82 1.36
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.844 r_dihedral_angle_4_deg 23.032 r_dihedral_angle_3_deg 11.943 r_scangle_it 7.281 r_scbond_it 4.77 r_dihedral_angle_1_deg 4.622 r_mcangle_it 2.732 r_mcbond_it 1.956 r_angle_refined_deg 1.44 r_angle_other_deg 0.863
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 24.844 r_dihedral_angle_4_deg 23.032 r_dihedral_angle_3_deg 11.943 r_scangle_it 7.281 r_scbond_it 4.77 r_dihedral_angle_1_deg 4.622 r_mcangle_it 2.732 r_mcbond_it 1.956 r_angle_refined_deg 1.44 r_angle_other_deg 0.863 r_mcbond_other 0.48 r_nbd_refined 0.322 r_symmetry_vdw_other 0.269 r_nbd_other 0.171 r_xyhbond_nbd_refined 0.171 r_symmetry_hbond_refined 0.132 r_chiral_restr 0.095 r_nbtor_other 0.082 r_symmetry_vdw_refined 0.078 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4870 Nucleic Acid Atoms Solvent Atoms 435 Heterogen Atoms 68
Software Software Software Name Purpose MOSFLM data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement