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Crystal structure of a putative oxidoreductase (PARMER_00841) from Parabacteroides merdae ATCC 43184 at 2.23 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 293 0.2M sodium acetate, 30.0% polyethylene glycol 4000, 0.1M tris hydrochloride pH 8.5, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.16 43.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 48.437 α = 90 b = 93.51 β = 90 c = 95.787 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2013-11-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97895,0.97959 SSRL BL11-1
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 2.23 27.528 96.2 0.076 9.24 21588 -3 36.759
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 2.23 2.31 95.3 0.558 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 MAD THROUGHOUT 2.23 27.528 21538 1103 98.35 0.1883 0.1863 0.1936 0.2235 0.2276 RANDOM 41.8434
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] -2.07 2.89 -0.82
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.829 r_dihedral_angle_4_deg 21.804 r_dihedral_angle_3_deg 15.313 r_dihedral_angle_1_deg 5.57 r_mcangle_it 3.055 r_mcbond_it 1.926 r_mcbond_other 1.925 r_angle_refined_deg 1.046 r_angle_other_deg 0.693 r_chiral_restr 0.064
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.829 r_dihedral_angle_4_deg 21.804 r_dihedral_angle_3_deg 15.313 r_dihedral_angle_1_deg 5.57 r_mcangle_it 3.055 r_mcbond_it 1.926 r_mcbond_other 1.925 r_angle_refined_deg 1.046 r_angle_other_deg 0.693 r_chiral_restr 0.064 r_bond_refined_d 0.006 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3465 Nucleic Acid Atoms Solvent Atoms 162 Heterogen Atoms
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