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Structure of Thermus thermophilus L-proline dehydrogenase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 295 100 mM MgCl2, 100 mM imidazole pH 7.0, 16% MPD, VAPOR DIFFUSION, SITTING DROP, temperature 295K
Crystal Properties Matthews coefficient Solvent content 2.28 45.99
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.067 α = 90 b = 89.59 β = 90 c = 94.316 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 2005-01-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 0.97932 ALS 4.2.2
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 47.16 98 0.079 13.6 6.24 46775
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 2.07 86.3 0.399 3 3.12
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 (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 47.16 46715 2356 98 0.192 0.192 0.19 0.1897 0.231 0.23 RANDOM 15.526
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] -0.32 -0.85 1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.351 r_dihedral_angle_4_deg 17.891 r_dihedral_angle_3_deg 15.333 r_dihedral_angle_1_deg 5.872 r_scangle_it 3.184 r_scbond_it 1.969 r_angle_refined_deg 1.542 r_mcangle_it 1.112 r_mcbond_it 0.715 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.351 r_dihedral_angle_4_deg 17.891 r_dihedral_angle_3_deg 15.333 r_dihedral_angle_1_deg 5.872 r_scangle_it 3.184 r_scbond_it 1.969 r_angle_refined_deg 1.542 r_mcangle_it 1.112 r_mcbond_it 0.715 r_nbtor_refined 0.303 r_nbd_refined 0.2 r_symmetry_vdw_refined 0.144 r_xyhbond_nbd_refined 0.139 r_chiral_restr 0.095 r_symmetry_hbond_refined 0.088 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4796 Nucleic Acid Atoms Solvent Atoms 250 Heterogen Atoms 138
Software Software Software Name Purpose d*TREK data scaling REFMAC refinement PDB_EXTRACT data extraction Blu-Ice data collection SOLVE phasing