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Crystal structure of carboxymuconolactone decarboxylase family protein possibly involved in oxygen detoxification (1591455) from METHANOCOCCUS JANNASCHII at 1.75 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 3.7 277 0.2M ammonium sulfate, 17.8% polyethylene glycol 300, 10.0% Glycerol, 0.1M phosphate-citrate pH 3.7, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.67 53.92
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.571 α = 90 b = 92.672 β = 90 c = 111.237 γ = 90
Symmetry Space Group C 2 2 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 2008-05-01 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97929,0.97907 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 1.75 28.952 99.5 0.078 0.078 4.8 4.9 38442
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 1.75 1.8 98.9 0.535 0.535 1.4 5 2789
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MAD THROUGHOUT 1.75 28.952 38417 1930 99.44 0.172 0.17 0.197 0.247 RANDOM 22.084
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] 0.13 0.3 -0.43
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.527 r_dihedral_angle_4_deg 25.592 r_dihedral_angle_3_deg 12.888 r_scangle_it 5.807 r_dihedral_angle_1_deg 4.807 r_scbond_it 4.576 r_mcangle_it 2.824 r_mcbond_it 1.961 r_angle_refined_deg 1.434 r_angle_other_deg 0.991
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.527 r_dihedral_angle_4_deg 25.592 r_dihedral_angle_3_deg 12.888 r_scangle_it 5.807 r_dihedral_angle_1_deg 4.807 r_scbond_it 4.576 r_mcangle_it 2.824 r_mcbond_it 1.961 r_angle_refined_deg 1.434 r_angle_other_deg 0.991 r_mcbond_other 0.444 r_symmetry_vdw_refined 0.325 r_symmetry_vdw_other 0.247 r_nbd_refined 0.221 r_symmetry_hbond_refined 0.214 r_nbtor_refined 0.179 r_nbd_other 0.169 r_xyhbond_nbd_refined 0.141 r_nbtor_other 0.087 r_chiral_restr 0.082 r_bond_refined_d 0.018 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2128 Nucleic Acid Atoms Solvent Atoms 104 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MOSFLM data reduction SHELXD phasing autoSHARP phasing