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Crystal Structure of DegV Family Protein Cg2579 from Corynebacterium glutamicum
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 295 0.2M Sodium formate, 20 % w/v Polyehtlyene glycol 3350, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 3.38 63.61
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.253 α = 90 b = 151.667 β = 90 c = 76.88 γ = 90
Symmetry Space Group P 21 21 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 ADSC QUANTUM 315 mirrors 2008-08-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9793 APS 19-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 2.4 49.3 100 0.12 7.8 8.7 47822 47822 37.7
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 2.4 2.44 100 0.716 2.5 7.3 2367
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) 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 2.41 49.3 45350 45350 2420 99.62 0.181 0.181 0.179 0.1872 0.218 0.224 RANDOM 31.381
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] 0.95 -0.02 -0.92
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.825 r_dihedral_angle_4_deg 20.051 r_dihedral_angle_3_deg 17.104 r_dihedral_angle_1_deg 6.103 r_scangle_it 4.42 r_scbond_it 2.688 r_angle_refined_deg 1.613 r_mcangle_it 1.525 r_mcbond_it 0.792 r_chiral_restr 0.099
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.825 r_dihedral_angle_4_deg 20.051 r_dihedral_angle_3_deg 17.104 r_dihedral_angle_1_deg 6.103 r_scangle_it 4.42 r_scbond_it 2.688 r_angle_refined_deg 1.613 r_mcangle_it 1.525 r_mcbond_it 0.792 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5935 Nucleic Acid Atoms Solvent Atoms 458 Heterogen Atoms 54
Software Software Software Name Purpose SBC-Collect data collection HKL-3000 data collection HKL-3000 phasing MLPHARE phasing DM model building SHELXD phasing RESOLVE model building Coot model building REFMAC refinement HKL-3000 data reduction HKL-3000 data scaling DM phasing RESOLVE phasing