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Crystal structure of a DUF1989 family protein (TM1040_0329) from SILICIBACTER SP. TM1040 at 1.35 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 277 22.0% PEG 3350, 0.1M Magnesium Chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.95 36.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.907 α = 90 b = 48.132 β = 98.44 c = 144.732 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 Flat mirror (vertical focusing); single crystal Si(111) bent monochromator (horizontal focusing) 2010-02-12 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837,0.97971,0.97941 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 58.798 85.8 0.086 0.086 11.1 6.6 152479 152479 10.84
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.35 1.42 100 0.625 0.625 2.3 5.7 25878
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 58.798 152408 5488 85.65 0.1387 0.1373 0.1373 0.1715 0.1695 RANDOM 15.5987
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] -0.19 0.33 0.54 -0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.025 r_dihedral_angle_4_deg 18.067 r_dihedral_angle_3_deg 12.039 r_dihedral_angle_1_deg 6.629 r_sphericity_free 6.605 r_scangle_it 4.02 r_sphericity_bonded 2.989 r_scbond_it 2.75 r_mcangle_it 1.976 r_angle_refined_deg 1.5
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.025 r_dihedral_angle_4_deg 18.067 r_dihedral_angle_3_deg 12.039 r_dihedral_angle_1_deg 6.629 r_sphericity_free 6.605 r_scangle_it 4.02 r_sphericity_bonded 2.989 r_scbond_it 2.75 r_mcangle_it 1.976 r_angle_refined_deg 1.5 r_mcbond_it 1.302 r_rigid_bond_restr 1.217 r_angle_other_deg 0.924 r_mcbond_other 0.562 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7052 Nucleic Acid Atoms Solvent Atoms 1086 Heterogen Atoms 13
Software Software Software Name Purpose XDS data scaling XSCALE data scaling MOSFLM data reduction SCALA data scaling SHELX phasing SHARP phasing SOLOMON phasing REFMAC refinement MolProbity model building PDB_EXTRACT data extraction XDS data reduction SHELXD phasing