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Crystal structure of Medicago truncatula N-carbamoylputrescine amidohydrolase (MtCPA) in complex with N-(dihydroxymethyl)putrescine
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 59.98
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 152.13 α = 90 b = 211.06 β = 90 c = 208.78 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 2015-08-06 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 1.97 40 98.3 0.098 10.45 4.2 462097 -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 1.97 2.1 91.2 0.74 1.95 4.2
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 THROUGHOUT 1ERZ 1.97 39.55 459786 2311 98.51 0.15808 0.1579 0.1676 0.19299 0.1967 RANDOM 33.576
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] 1.14 0.03 -1.17
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.243 r_dihedral_angle_4_deg 18.214 r_dihedral_angle_3_deg 12.287 r_long_range_B_refined 7.351 r_long_range_B_other 7.351 r_dihedral_angle_1_deg 5.765 r_scangle_other 1.851 r_angle_refined_deg 1.507 r_mcangle_it 1.358 r_mcangle_other 1.358
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.243 r_dihedral_angle_4_deg 18.214 r_dihedral_angle_3_deg 12.287 r_long_range_B_refined 7.351 r_long_range_B_other 7.351 r_dihedral_angle_1_deg 5.765 r_scangle_other 1.851 r_angle_refined_deg 1.507 r_mcangle_it 1.358 r_mcangle_other 1.358 r_scbond_it 1.189 r_scbond_other 1.189 r_angle_other_deg 0.904 r_mcbond_it 0.799 r_mcbond_other 0.799 r_chiral_restr 0.09 r_gen_planes_refined 0.021 r_gen_planes_other 0.017 r_bond_refined_d 0.015 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 37591 Nucleic Acid Atoms Solvent Atoms 4399 Heterogen Atoms 425
Software Software Software Name Purpose REFMAC refinement XSCALE data scaling XDS data reduction BALBES phasing RESOLVE model building