☰ Navigation Tabs
Crystal structure of mouse 1-pyrroline-5-carboxylate dehydrogenase complexed with the product glutamate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3V9J PDB ENTRY 3V9J
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 reservoir: 20-25% w/v PEG3350, 0.2 M lithium sulfate, 0.1 M Bis-Tris, pH 6.5, cryoprotectant: 25% glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.13 42.15
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.82 α = 90 b = 93.954 β = 90 c = 132.241 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 100 CCD NOIR-1 2011-04-27 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 4.2.2 1.0000 ALS 4.2.2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.501 46.977 99.6 0.066 25.3 7.3 168017 168017
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 1.501 1.58 97.4 0.418 0.418 6.7 23728
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 3V9J 1.501 46.977 167897 8509 99.6 0.1523 0.1513 0.149 0.1691 0.1668 SAME TEST SET AS PDB ENTRY 3V9J 11.1311
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] -1.3483 1.8693 -0.259
RMS Deviations Key Refinement Restraint Deviation f_dihedral_angle_d 11.672 f_angle_d 1.091 f_chiral_restr 0.071 f_bond_d 0.006 f_plane_restr 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8157 Nucleic Acid Atoms Solvent Atoms 896 Heterogen Atoms 32
Software Software Software Name Purpose SCALA data scaling PHENIX refinement PDB_EXTRACT data extraction Blu-Ice data collection XDS data reduction MOLREP phasing PHASER phasing