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Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) in complex with cadaverine
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ERZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 292 20% PEG3350, 8% Tacsimate at pH 7.0, 10% glycerol
Crystal Properties Matthews coefficient Solvent content 3.07 59.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.269 α = 90 b = 211.041 β = 90 c = 208.822 γ = 90
Symmetry Space Group P 21 21 2
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 RAYONIX MX300-HS 2015-08-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.000 APS 22-ID
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 2.19 40 99.1 0.108 10.1 4.16 340107 -3
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 2.19 2.32 95.3 0.754 1.93 4.1
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 1ERZ 2.19 39.56 336704 3402 99.09 0.172 0.171 0.1807 0.211 0.2169 RANDOM 52.15
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] 0.1 -0.65 0.55
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.381 r_dihedral_angle_4_deg 16.256 r_dihedral_angle_3_deg 11.447 r_long_range_B_refined 8.701 r_long_range_B_other 8.7 r_dihedral_angle_1_deg 4.3 r_angle_refined_deg 1.6 r_scangle_other 1.499 r_mcangle_it 1.266 r_mcangle_other 1.266
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.381 r_dihedral_angle_4_deg 16.256 r_dihedral_angle_3_deg 11.447 r_long_range_B_refined 8.701 r_long_range_B_other 8.7 r_dihedral_angle_1_deg 4.3 r_angle_refined_deg 1.6 r_scangle_other 1.499 r_mcangle_it 1.266 r_mcangle_other 1.266 r_scbond_it 0.943 r_scbond_other 0.943 r_angle_other_deg 0.911 r_mcbond_it 0.73 r_mcbond_other 0.73 r_chiral_restr 0.114 r_gen_planes_refined 0.02 r_bond_refined_d 0.018 r_gen_planes_other 0.016 r_bond_other_d 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 37395 Nucleic Acid Atoms Solvent Atoms 3242 Heterogen Atoms 301
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction BALBES phasing