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Crystal structure of ytaA (2635576) from Bacillus subtilis at 2.50 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.57 277 NANODROP, 2.23M Ammonium sulfate, 0.1M Citric acid pH 5.57, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 172.999 α = 90 b = 172.999 β = 90 c = 192.574 γ = 120
Symmetry Space Group P 64 2 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 Flat mirror (vertical focusing) 2007-05-04 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 0.91837, 0.97904, 0.97932 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 2.5 29.961 99.9 0.126 0.126 4.6 10.8 59155 50.53
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 2.5 2.56 100 0.864 0.864 0.9 11 4302
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 2.5 29.961 59108 2988 99.91 0.199 0.198 0.2 0.21 0.2122 RANDOM 40.685
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] -0.36 -0.18 -0.36 0.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.805 r_dihedral_angle_3_deg 9.171 r_dihedral_angle_4_deg 9.125 r_scangle_it 6.54 r_scbond_it 4.356 r_mcangle_it 2.556 r_dihedral_angle_1_deg 2.155 r_angle_refined_deg 1.655 r_mcbond_it 1.517 r_angle_other_deg 1.182
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.805 r_dihedral_angle_3_deg 9.171 r_dihedral_angle_4_deg 9.125 r_scangle_it 6.54 r_scbond_it 4.356 r_mcangle_it 2.556 r_dihedral_angle_1_deg 2.155 r_angle_refined_deg 1.655 r_mcbond_it 1.517 r_angle_other_deg 1.182 r_mcbond_other 0.321 r_symmetry_hbond_refined 0.206 r_nbd_refined 0.178 r_nbtor_refined 0.173 r_xyhbond_nbd_refined 0.16 r_nbd_other 0.131 r_symmetry_vdw_refined 0.101 r_symmetry_vdw_other 0.092 r_nbtor_other 0.083 r_chiral_restr 0.067 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5286 Nucleic Acid Atoms Solvent Atoms 187 Heterogen Atoms 113
Software Software Software Name Purpose REFMAC refinement PHENIX refinement MolProbity model building SCALA data scaling PDB_EXTRACT data extraction MAR345 data collection MOSFLM data reduction SOLVE phasing RESOLVE phasing