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Crystal structure of Cg10062 inactivated by (S)-oxirane-2-carboxylate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3N4G PDB ENTRY 3N4G
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4 298 6 micro liter hanging drop consisting of equal volume of crystallization solution (3% PEG 6000, pH 4.0) and protein solution (18.1mg/L Cg10062 in 10mM Tris-SO4, pH 8.0), vapor diffusion, hanging drop, temperature 298K
Crystal Properties Matthews coefficient Solvent content 1.64 25.18
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 49.435 α = 90 b = 49.435 β = 90 c = 80.175 γ = 120
Symmetry Space Group P 3 2 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 IMAGE PLATE RIGAKU RAXIS IV++ 2005-09-04 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RU200 1.5418
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 99.8 0.048 64.887 11.3 7841
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 2.09 100 0.427 8.6 11.3 766
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 3N4G 2.02 25 7835 362 99.87 0.169 0.166 0.236 0.2505 RANDOM 35.552
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.282 r_dihedral_angle_4_deg 22.478 r_dihedral_angle_3_deg 16.822 r_dihedral_angle_1_deg 14.891 r_sphericity_free 4.94 r_scangle_it 4.755 r_scbond_it 3.66 r_rigid_bond_restr 3.271 r_sphericity_bonded 3.228 r_mcangle_it 2.135
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.282 r_dihedral_angle_4_deg 22.478 r_dihedral_angle_3_deg 16.822 r_dihedral_angle_1_deg 14.891 r_sphericity_free 4.94 r_scangle_it 4.755 r_scbond_it 3.66 r_rigid_bond_restr 3.271 r_sphericity_bonded 3.228 r_mcangle_it 2.135 r_angle_refined_deg 1.728 r_mcbond_it 1.407 r_symmetry_vdw_refined 0.355 r_nbtor_refined 0.304 r_nbd_refined 0.268 r_symmetry_hbond_refined 0.24 r_xyhbond_nbd_refined 0.189 r_chiral_restr 0.122 r_bond_refined_d 0.018 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 944 Nucleic Acid Atoms Solvent Atoms 104 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