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Crystal structure of Cg10062 inactivated by(R)-oxirane-2-carboxylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2FLT PDB ENTRY 2FLT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 298 6 micro liter hanging drop consisting of equal volume of crystallization solution (0.07 M sodium aetate buffer, pH 4.6, 1.4 M sodium chloride) and protein solution (18.9mg/L Cg10062 in 10mM Tris-SO4, pH 8.0), Hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.17 43.23
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.099 α = 90 b = 131.002 β = 90 c = 179.393 γ = 90
Symmetry Space Group P 21 21 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 IMAGE PLATE RIGAKU RAXIS IV++ 2005-09-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.54178
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 2.02 50 99.9 0.131 61.2 11.4 89329
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 2.02 2.09 99.9 0.506 1.206 11.4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model 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 MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2FLT 2.54 45 43020 2312 99.96 0.22446 0.22343 0.2242 0.24327 0.2437 RANDOM 36.627
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] -0.27 -0.11 0.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.326 r_dihedral_angle_4_deg 16.69 r_dihedral_angle_3_deg 15.312 r_scangle_it 3.26 r_mcangle_it 2.551 r_scbond_it 2.16 r_mcbond_it 1.393 r_angle_refined_deg 1.337 r_dihedral_angle_1_deg 1.143 r_nbtor_refined 0.328
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 42.326 r_dihedral_angle_4_deg 16.69 r_dihedral_angle_3_deg 15.312 r_scangle_it 3.26 r_mcangle_it 2.551 r_scbond_it 2.16 r_mcbond_it 1.393 r_angle_refined_deg 1.337 r_dihedral_angle_1_deg 1.143 r_nbtor_refined 0.328 r_xyhbond_nbd_refined 0.322 r_nbd_refined 0.305 r_symmetry_vdw_refined 0.288 r_symmetry_hbond_refined 0.245 r_chiral_restr 0.089 r_bond_refined_d 0.007 r_gen_planes_refined 0.007 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 10546 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing