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Crystal Analysis of 1-Pyrroline-5-Carboxylate Dehydrogenase from Thermus with bound NADH
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1UZB PDB ENTRY 1UZB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 5.2 PROTEIN WAS CRYSTALLIZED FROM 36% MPD, 50 MM SODIUM CITRATE/HCL, PH 5.2; THEN SOAKED IN 1 MM NAD,CA.5MM DELTA1-PYRROLINE-5 CARBOXYLATE AND 50 MM SODIUM ACETATE/HCL, PH 5.2.
Crystal Properties Matthews coefficient Solvent content 2.5 50.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.007 α = 90 b = 102.007 β = 90 c = 278.319 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 IMAGE PLATE RIGAKU IMAGE PLATE MIRRORS 2004-02-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 SPring-8 BL26B1
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 1.9 40 100 0.08 17.26 4 85247 -3 13.4
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 1.94 100 0.46 2.15 3
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 1UZB 1.9 37.29 82153 4178 96.5 0.176 0.176 0.1761 0.212 0.2093 RANDOM 25.4
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] 6.15 3.96 6.15 -12.3
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 2.9 c_scbond_it 2 c_mcangle_it 1.54 c_angle_deg 1.4 c_mcbond_it 1.11 c_improper_angle_d 0.89 c_bond_d 0.007 c_bond_d_na c_bond_d_prot
RMS Deviations Key Refinement Restraint Deviation c_dihedral_angle_d 22.7 c_scangle_it 2.9 c_scbond_it 2 c_mcangle_it 1.54 c_angle_deg 1.4 c_mcbond_it 1.11 c_improper_angle_d 0.89 c_bond_d 0.007 c_bond_d_na c_bond_d_prot c_angle_d c_angle_d_na c_angle_d_prot c_angle_deg_na c_angle_deg_prot c_dihedral_angle_d_na c_dihedral_angle_d_prot c_improper_angle_d_na c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8075 Nucleic Acid Atoms Solvent Atoms 808 Heterogen Atoms 80
Software Software Software Name Purpose CNS refinement HKL-2000 data reduction SCALEPACK data scaling CNS phasing