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The crystal structure of YcgJ protein from Bacillus subitilis at 2.1 A resolution
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 2.4M Am Sulfate, 0.1M Na Citrate , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.03 59.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 69.928 α = 90 b = 74.212 β = 90 c = 246.161 γ = 90
Symmetry Space Group C 2 2 21
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 MAR CCD 165 mm Diamond monochromator and horizontal, vertical focusing mirrors 2004-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID 0.9793 APS 31-ID
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 2.1 20 99.9 0.099 16.66 6.43 37699 37661 -3 28.5
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) 2.1 2.17 100 0.258 9.35 6.75 3711
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2.1 20 -3 37652 35769 1883 99.78 0.17872 0.17872 0.17638 0.1897 0.22423 0.2351 RANDOM 17.301
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] 0.54 0.22 -0.76
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.959 r_dihedral_angle_4_deg 19.962 r_dihedral_angle_3_deg 15.468 r_dihedral_angle_1_deg 6.057 r_scangle_it 3.954 r_scbond_it 2.689 r_mcangle_it 1.442 r_angle_refined_deg 1.345 r_mcbond_it 1.26 r_angle_other_deg 0.828
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.959 r_dihedral_angle_4_deg 19.962 r_dihedral_angle_3_deg 15.468 r_dihedral_angle_1_deg 6.057 r_scangle_it 3.954 r_scbond_it 2.689 r_mcangle_it 1.442 r_angle_refined_deg 1.345 r_mcbond_it 1.26 r_angle_other_deg 0.828 r_xyhbond_nbd_other 0.264 r_symmetry_hbond_refined 0.244 r_symmetry_vdw_other 0.216 r_nbd_refined 0.208 r_mcbond_other 0.199 r_nbd_other 0.19 r_xyhbond_nbd_refined 0.173 r_nbtor_refined 0.172 r_symmetry_vdw_refined 0.11 r_nbtor_other 0.088 r_chiral_restr 0.083 r_bond_refined_d 0.014 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3722 Nucleic Acid Atoms Solvent Atoms 327 Heterogen Atoms 40
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling SOLVE phasing