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Crystal structure of Medicago truncatula (delta)1-Pyrroline-5-Carboxylate Reductase (MtP5CR) in complex with NAD+
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IZZ 2IZZ, 5BSE experimental model PDB 5BSE 2IZZ, 5BSE
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 2.92 57.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.54 α = 67.5 b = 100.78 β = 85.86 c = 101.61 γ = 89.78
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 1.85 40 97.4 0.045 0.053 17.69 3.7 266309 -3 35.2
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 1.85 1.9 96.2 0.64 0.75 1.96 3.7
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2IZZ, 5BSE 1.85 39.13 264178 2131 97.51 0.156 0.155 0.177 0.1803 RANDOM 41.4
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] -1.1 -0.42 -1.23 -0.47 0.91 1.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.699 r_dihedral_angle_4_deg 16.244 r_dihedral_angle_3_deg 12.893 r_dihedral_angle_1_deg 5.998 r_mcangle_it 4.119 r_mcbond_it 2.95 r_mcbond_other 2.949 r_angle_other_deg 1.972 r_angle_refined_deg 1.864 r_chiral_restr 0.112
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.699 r_dihedral_angle_4_deg 16.244 r_dihedral_angle_3_deg 12.893 r_dihedral_angle_1_deg 5.998 r_mcangle_it 4.119 r_mcbond_it 2.95 r_mcbond_other 2.949 r_angle_other_deg 1.972 r_angle_refined_deg 1.864 r_chiral_restr 0.112 r_bond_refined_d 0.021 r_gen_planes_refined 0.012 r_bond_other_d 0.01 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19785 Nucleic Acid Atoms Solvent Atoms 1670 Heterogen Atoms 580
Software Software Software Name Purpose XSCALE data scaling REFMAC refinement PDB_EXTRACT data extraction XDS data reduction