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Crystal structure of a DUF5037 family protein (RUMGNA_01148) from Ruminococcus gnavus ATCC 29149 at 2.55 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 0.08M sodium cacodylate pH 6.5, 20% glycerol, 16% polyethylene glycol 8000, 0.16M magnesium acetate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.83 56.56
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 148.653 α = 90 b = 84.139 β = 98.31 c = 53.031 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 MARMOSAIC 325 mm CCD double crystal monochromator 2012-05-03 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL9-2 0.91162,0.97922 SSRL BL9-2
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 2.55 45.971 99.8 0.076 12.84 21164 -3 62.923
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 2.55 2.64 100 0.739 2.1
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 MAD THROUGHOUT 2.55 45.971 21159 1088 99.72 0.1899 0.1883 0.1933 0.218 0.2214 RANDOM 61.0088
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] 3.91 3.53 -4.81 1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.916 r_dihedral_angle_4_deg 19.905 r_dihedral_angle_3_deg 11.245 r_dihedral_angle_1_deg 3.608 r_angle_refined_deg 1.646 r_angle_other_deg 1.404 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.916 r_dihedral_angle_4_deg 19.905 r_dihedral_angle_3_deg 11.245 r_dihedral_angle_1_deg 3.608 r_angle_refined_deg 1.646 r_angle_other_deg 1.404 r_chiral_restr 0.098 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.004 r_gen_planes_other 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3893 Nucleic Acid Atoms Solvent Atoms 26 Heterogen Atoms 18
Software Software Software Name Purpose MolProbity model building PDB_EXTRACT data extraction SHELX phasing SHARP phasing XSCALE data scaling REFMAC refinement XDS data reduction SHELXD phasing