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Crystal structure of a biotin protein ligase-like protein of unknown function (tm1040_0394) from silicibacter sp. tm1040 at 1.70 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 277 NANODROP, 0.2M Ca(OAc)2, 40.0% PEG 400, 0.1M HEPES pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.19 43.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.76 α = 90 b = 36.56 β = 99.28 c = 71 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 300 mm CCD Adjustable focusing mirrors in K-B geometry 2007-10-26 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-D 0.91840, 0.97953, 0.97939 APS 23-ID-D
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 1.7 29.553 97.5 0.076 7.08 3.33 24223 -3 21.03
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 1.7 1.8 95.1 0.532 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 1.7 29.553 24219 1211 98.78 0.182 0.179 0.1843 0.226 0.2291 RANDOM 20.605
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] 0.03 0.71 -0.44 0.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.898 r_dihedral_angle_4_deg 15.23 r_dihedral_angle_3_deg 13.139 r_scangle_it 7.548 r_dihedral_angle_1_deg 5.641 r_scbond_it 5.148 r_mcangle_it 3.237 r_mcbond_it 2.14 r_angle_refined_deg 1.458 r_angle_other_deg 0.931
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.898 r_dihedral_angle_4_deg 15.23 r_dihedral_angle_3_deg 13.139 r_scangle_it 7.548 r_dihedral_angle_1_deg 5.641 r_scbond_it 5.148 r_mcangle_it 3.237 r_mcbond_it 2.14 r_angle_refined_deg 1.458 r_angle_other_deg 0.931 r_mcbond_other 0.56 r_symmetry_vdw_other 0.237 r_symmetry_hbond_refined 0.217 r_nbd_refined 0.216 r_nbd_other 0.203 r_symmetry_vdw_refined 0.19 r_nbtor_refined 0.177 r_xyhbond_nbd_refined 0.153 r_nbtor_other 0.088 r_chiral_restr 0.077 r_metal_ion_refined 0.055 r_bond_refined_d 0.015 r_symmetry_metal_ion_refined 0.006 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1704 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 14
Software Software Software Name Purpose REFMAC refinement PHENIX refinement SHELX phasing MolProbity model building XSCALE data scaling PDB_EXTRACT data extraction MAR345 data collection XDS data reduction SHELXD phasing SHARP phasing