☰ Navigation Tabs
Crystal structure of Medicago truncatula (delta)1-Pyrroline-5-Carboxylate Reductase (MtP5CR)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IZZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 292 Morpheus screen (Molecular Dimensions) A7 solution (100 mM HEPES/MOPS buffer pH 7.5, 10% polyethylene glycol 4000, 20% glycerol, 30 mM MgCl2 and 30 mM CaCl2).
Crystal Properties Matthews coefficient Solvent content 2.89 57.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 86.8 α = 67.9 b = 100.6 β = 85.3 c = 101.2 γ = 89.3
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 315r 2014-11-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9790 APS 19-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.7 40 97.2 0.044 0.05 15.17 4.1 338502 -3 44.7
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.7 1.74 95.6 0.67 0.799 1.9 3.4
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 FREE R-VALUE 2IZZ 1.7 38.93 335794 2708 97.32 0.16 0.16 0.1691 0.18 0.1838 RANDOM 52.8
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] -1.41 -0.29 -0.43 -0.08 -0.44 0.78
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.583 r_dihedral_angle_4_deg 15.294 r_dihedral_angle_3_deg 12.677 r_dihedral_angle_1_deg 5.86 r_mcangle_it 4.096 r_mcbond_other 2.964 r_mcbond_it 2.963 r_angle_refined_deg 1.9 r_angle_other_deg 1.696 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.583 r_dihedral_angle_4_deg 15.294 r_dihedral_angle_3_deg 12.677 r_dihedral_angle_1_deg 5.86 r_mcangle_it 4.096 r_mcbond_other 2.964 r_mcbond_it 2.963 r_angle_refined_deg 1.9 r_angle_other_deg 1.696 r_chiral_restr 0.112 r_bond_refined_d 0.02 r_bond_other_d 0.013 r_gen_planes_refined 0.013 r_gen_planes_other 0.01
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19793 Nucleic Acid Atoms Solvent Atoms 1471 Heterogen Atoms 75
Software Software Software Name Purpose XDS data reduction REFMAC refinement PDB_EXTRACT data extraction XSCALE data scaling PHASER phasing