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Crystal structure of protein DIP2346 from Corynebacterium diphtheriae
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6 294 100mM Bis-Tris pH 6.0, 30% PEG 3350, 200mM Ammonium acetate, 10% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 294K
Crystal Properties Matthews coefficient Solvent content 2.58 52.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 95.453 α = 90 b = 138.936 β = 116.49 c = 98.266 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 77 CCD MAR CCD 165 mm 2005-02-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
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 2.51 50 97.6 0.1 0.081 4.4 2.6 78192 -0.5 59.6
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 2.51 2.61 81.1 0.58 1.1 2.1
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 2.51 20 75434 1542 98.68 0.21188 0.21068 0.2124 0.27134 0.2668 RANDOM 62.536
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] -0.83 -1.52 -1.37 0.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.383 r_dihedral_angle_3_deg 19.233 r_dihedral_angle_4_deg 15.37 r_scangle_it 14.903 r_scbond_it 11.831 r_mcangle_it 7.336 r_mcbond_it 5.348 r_dihedral_angle_1_deg 5.289 r_angle_refined_deg 1.146 r_nbtor_refined 0.292
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.383 r_dihedral_angle_3_deg 19.233 r_dihedral_angle_4_deg 15.37 r_scangle_it 14.903 r_scbond_it 11.831 r_mcangle_it 7.336 r_mcbond_it 5.348 r_dihedral_angle_1_deg 5.289 r_angle_refined_deg 1.146 r_nbtor_refined 0.292 r_symmetry_hbond_refined 0.213 r_xyhbond_nbd_refined 0.138 r_nbd_refined 0.135 r_symmetry_vdw_refined 0.124 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other 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 15076 Nucleic Acid Atoms Solvent Atoms 117 Heterogen Atoms 24
Software Software Software Name Purpose SHELX model building REFMAC refinement MAR345 data collection HKL-2000 data reduction HKL-2000 data scaling SHELX phasing