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Crystal structure of a domain of unknown function, DUF4425 (BVU_3708) from Bacteroides vulgatus ATCC 8482 at 1.35 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 0.1M HEPES pH 7.5, 1.4M tri-sodium citrate, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 1.96 37.29
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.237 α = 90 b = 99.302 β = 90 c = 41.085 γ = 90
Symmetry Space Group P 21 21 2
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 Vertical focusing mirror; double crystal Si(111) monochromator 2011-07-18 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL14-1 0.96109,0.97961 SSRL BL14-1
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 1.35 27.96 93.6 0.027 14.43 45712 -3 19.297
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 1.35 1.4 87.9 0.599 1.4
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 1.35 27.96 45670 2302 95.75 0.1592 0.1567 0.1632 0.2067 0.2107 RANDOM 23.0605
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] 0.23 -0.22
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.201 r_sphericity_free 21.947 r_dihedral_angle_4_deg 13.843 r_dihedral_angle_3_deg 12.498 r_rigid_bond_restr 9.591 r_sphericity_bonded 9.116 r_dihedral_angle_1_deg 6.247 r_angle_refined_deg 1.252 r_angle_other_deg 0.79 r_chiral_restr 0.086
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.201 r_sphericity_free 21.947 r_dihedral_angle_4_deg 13.843 r_dihedral_angle_3_deg 12.498 r_rigid_bond_restr 9.591 r_sphericity_bonded 9.116 r_dihedral_angle_1_deg 6.247 r_angle_refined_deg 1.252 r_angle_other_deg 0.79 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1843 Nucleic Acid Atoms Solvent Atoms 244 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 autoSHARP phasing