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Crystal structure of an antioxidant defense protein (mlr4105) from mesorhizobium loti maff303099 at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 277 NANODROP, 20.0% PEG 6000, 0.1M Tris-HCl pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K 2 VAPOR DIFFUSION, SITTING DROP 6.2 277 NANODROP, 0.2M NaCl, 50.0% PEG 200, 0.1M Na,K Phosphate pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.69 α = 90 b = 68.06 β = 95.94 c = 266.83 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 MARMOSAIC 325 mm CCD Flat mirror (vertical focusing) 2007-02-11 M SINGLE WAVELENGTH 2 2 x-ray 100 CCD MARMOSAIC 300 mm CCD Adjustable focusing mirrors in K-B geometry 2007-08-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837 SSRL BL11-1 2 SYNCHROTRON APS BEAMLINE 23-ID-D 0.97942 APS 23-ID-D
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 2 29.814 84.6 0.058 7.38 138837 -3 21.909
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 2 2.07 41.9 0.354 1.6
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION SAD + MOLECULAR REPLACEMENT THROUGHOUT 2 29.814 138822 6959 87.53 0.174 0.171 0.1762 0.225 0.2268 RANDOM 24.95
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] -0.31 -0.04 0.25 0.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.995 r_dihedral_angle_3_deg 15.072 r_dihedral_angle_4_deg 13.86 r_scangle_it 5.879 r_dihedral_angle_1_deg 5.846 r_scbond_it 4.223 r_mcangle_it 2.248 r_angle_refined_deg 1.498 r_mcbond_it 1.466 r_angle_other_deg 0.992
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.995 r_dihedral_angle_3_deg 15.072 r_dihedral_angle_4_deg 13.86 r_scangle_it 5.879 r_dihedral_angle_1_deg 5.846 r_scbond_it 4.223 r_mcangle_it 2.248 r_angle_refined_deg 1.498 r_mcbond_it 1.466 r_angle_other_deg 0.992 r_mcbond_other 0.711 r_chiral_restr 0.087 r_bond_refined_d 0.016 r_gen_planes_refined 0.007 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16600 Nucleic Acid Atoms Solvent Atoms 731 Heterogen Atoms 176
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MolProbity model building PDB_EXTRACT data extraction MAR345 data collection XDS data reduction MOSFLM data reduction XSCALE data scaling SCALA data scaling SHARP phasing MOLREP phasing