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Crystal structure of a DUF4466 family protein (PARMER_03218) from Parabacteroides merdae ATCC 43184 at 2.00 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.6 277 5.0% Glycerol, 19.0% polyethylene glycol 4000, 19.0% 2-propanol, 0.1M sodium citrate pH 5.6, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.5 50.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 62.749 α = 90 b = 85.879 β = 90 c = 128.695 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 Rhodium-coated vertical and horizontal focusing mirrors; liquid-nitrogen cooled double crystal Si(111) monochromator 2012-03-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL12-2 SSRL BL12-2
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 29.469 97.8 0.07 9.67 47406 -3 32.338
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 2.07 97.5 0.706 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 THROUGHOUT 2 29.469 47345 2396 99.12 0.1764 0.1742 0.1811 0.2161 0.2255 RANDOM 51.4653
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] 0.1 1.2 -1.3
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.406 r_dihedral_angle_3_deg 13.759 r_dihedral_angle_4_deg 10.765 r_dihedral_angle_1_deg 6.686 r_angle_refined_deg 1.702 r_angle_other_deg 1.185 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.406 r_dihedral_angle_3_deg 13.759 r_dihedral_angle_4_deg 10.765 r_dihedral_angle_1_deg 6.686 r_angle_refined_deg 1.702 r_angle_other_deg 1.185 r_chiral_restr 0.104 r_bond_refined_d 0.016 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4641 Nucleic Acid Atoms Solvent Atoms 355 Heterogen Atoms 6
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