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Crystal structure of Medicago truncatula (delta)1-Pyrroline-5-Carboxylate Reductase (MtP5CR) in complex with NADP+
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 57.41
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.239 α = 68.13 b = 100.3 β = 85.76 c = 100.786 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 2014-11-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 19-ID 0.9786 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 1.95 40 96.9 0.113 0.136 10.74 3.2 225659 -3 28.9
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 1.95 2.06 92.5 0.728 0.876 1.98 3.2
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 1.95 39.39 223400 2257 97.04 0.156 0.155 0.1667 0.178 0.188 RANDOM 31.34
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] -0.29 -0.79 0.02 0.29 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.733 r_dihedral_angle_4_deg 16.559 r_dihedral_angle_3_deg 12.296 r_dihedral_angle_1_deg 5.706 r_mcangle_it 2.646 r_angle_refined_deg 1.826 r_mcbond_it 1.797 r_mcbond_other 1.794 r_angle_other_deg 1.706 r_chiral_restr 0.101
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.733 r_dihedral_angle_4_deg 16.559 r_dihedral_angle_3_deg 12.296 r_dihedral_angle_1_deg 5.706 r_mcangle_it 2.646 r_angle_refined_deg 1.826 r_mcbond_it 1.797 r_mcbond_other 1.794 r_angle_other_deg 1.706 r_chiral_restr 0.101 r_bond_refined_d 0.019 r_bond_other_d 0.011 r_gen_planes_refined 0.011 r_gen_planes_other 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 19777 Nucleic Acid Atoms Solvent Atoms 1964 Heterogen Atoms 620
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling PDB_EXTRACT data extraction