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Crystal analysis of delta1-pyrroline-5-carboxylate dehydrogenase from Thermus thermophilus with bound L-proline
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2BHQ PDB ENTRY 2bhq
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.2 293 30% MPD, 50MM SODIUM CITRATE/HCL, PH5.2; THEN SOAKED IN 30% MPD, 50mM L-proline, 50MM SODIUM Acetate, PH5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.19
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 100.349 α = 90 b = 100.349 β = 90 c = 279.993 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210 mirrors 2006-11-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44B2 1.0 SPring-8 BL44B2
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 25 100 0.069 0.063 24.4 5.7 82759 82759 -3 17.1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.9 1.97 100 0.306 0.277 5.2 5.5 8315
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 2bhq 1.9 24.61 75124 75124 3970 95.51 0.15868 0.15693 0.1568 0.19157 0.1906 RANDOM 17.153
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] 1.09 0.55 1.09 -1.64
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.103 r_dihedral_angle_4_deg 16.59 r_dihedral_angle_3_deg 13.632 r_dihedral_angle_1_deg 6.212 r_scangle_it 3.639 r_scbond_it 2.202 r_angle_refined_deg 1.377 r_mcangle_it 1.159 r_mcbond_it 0.665 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.103 r_dihedral_angle_4_deg 16.59 r_dihedral_angle_3_deg 13.632 r_dihedral_angle_1_deg 6.212 r_scangle_it 3.639 r_scbond_it 2.202 r_angle_refined_deg 1.377 r_mcangle_it 1.159 r_mcbond_it 0.665 r_nbtor_refined 0.311 r_metal_ion_refined 0.278 r_nbd_refined 0.199 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.18 r_xyhbond_nbd_refined 0.132 r_chiral_restr 0.095 r_bond_refined_d 0.014 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8076 Nucleic Acid Atoms Solvent Atoms 757 Heterogen Atoms 106
Software Software Software Name Purpose REFMAC refinement BSS data collection HKL-2000 data reduction HKL-2000 data scaling REFMAC phasing