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Structure of Thermus thermophilus Proline Dehydrogenase inactivated by N-propargylglycine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2G37 PDB entry 2G37
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 100MM MGCL2, 100MM IMIDAZOLE PH=7.0, 14% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.26 45.65
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.383 α = 90 b = 90.104 β = 90 c = 94.83 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 173 CCD NOIR-1 beamline optics 2007-02-12 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0 ALS 4.2.2
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 1.9 41.96 99.3 0.059 0.059 12.5 5.82 55959 28.3
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 1.9 1.97 100 0.356 3.3 5.78 5556
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 2G37 1.9 41.1 55878 2817 99.26 0.196 0.195 0.1938 0.222 0.2188 RANDOM 32.299
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] 0.18 -1.28 1.1
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.829 r_dihedral_angle_4_deg 15.839 r_dihedral_angle_3_deg 14.158 r_dihedral_angle_1_deg 4.913 r_scangle_it 3.093 r_scbond_it 1.909 r_angle_refined_deg 1.314 r_mcangle_it 1.031 r_mcbond_it 0.64 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.829 r_dihedral_angle_4_deg 15.839 r_dihedral_angle_3_deg 14.158 r_dihedral_angle_1_deg 4.913 r_scangle_it 3.093 r_scbond_it 1.909 r_angle_refined_deg 1.314 r_mcangle_it 1.031 r_mcbond_it 0.64 r_nbtor_refined 0.304 r_nbd_refined 0.195 r_symmetry_vdw_refined 0.186 r_xyhbond_nbd_refined 0.122 r_chiral_restr 0.087 r_symmetry_hbond_refined 0.087 r_bond_refined_d 0.011 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4750 Nucleic Acid Atoms Solvent Atoms 334 Heterogen Atoms 138
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection d*TREK data reduction