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Crystal structure of YkqA from Bacillus subtilis. Northeast Structural Genomics Target SR631
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 MICROBATCH UNDER OIL 277 0.1 M NaCl, 0.1 Na Citrate, 60% PEG 400, MICROBATCH UNDER OIL, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.9125 35.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.577 α = 90 b = 62.131 β = 101.69 c = 55.527 γ = 90
Symmetry Space Group P 1 21 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 ADSC QUANTUM 4 mirrors 2007-05-31 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSLS BEAMLINE X4A 0.97900 NSLS X4A
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 50 99 0.041 18.8 3.8 55141 -3
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) 1.35 1.4 99.7 0.179 3.6 11083
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 1.35 19.35 55139 2801 97.83 0.133 0.131 0.2125 0.176 0.2327 RANDOM 12.597
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] 0.07 -0.17 -0.22 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.399 r_sphericity_free 16.723 r_dihedral_angle_4_deg 14.389 r_dihedral_angle_3_deg 13.158 r_scangle_it 6.405 r_dihedral_angle_1_deg 6.376 r_sphericity_bonded 5.757 r_scbond_it 5.173 r_mcangle_it 3.506 r_mcbond_it 3.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.399 r_sphericity_free 16.723 r_dihedral_angle_4_deg 14.389 r_dihedral_angle_3_deg 13.158 r_scangle_it 6.405 r_dihedral_angle_1_deg 6.376 r_sphericity_bonded 5.757 r_scbond_it 5.173 r_mcangle_it 3.506 r_mcbond_it 3.04 r_rigid_bond_restr 2.515 r_angle_refined_deg 2.056 r_angle_other_deg 0.973 r_mcbond_other 0.968 r_symmetry_vdw_refined 0.32 r_symmetry_vdw_other 0.299 r_nbd_refined 0.229 r_nbd_other 0.21 r_nbtor_refined 0.197 r_symmetry_hbond_refined 0.19 r_xyhbond_nbd_refined 0.176 r_chiral_restr 0.145 r_nbtor_other 0.09 r_bond_refined_d 0.025 r_gen_planes_refined 0.012 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2227 Nucleic Acid Atoms Solvent Atoms 446 Heterogen Atoms 13
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling SOLVE phasing RESOLVE phasing REFMAC refinement PDB_EXTRACT data extraction ADSC data collection HKL-2000 data reduction HKL-2000 data scaling