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Crystal structure of Medicago truncatula ATP-phosphoribosyltransferase in relaxed form
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.3 292 2.63 M NaCl, 100 mM Bis-Tris propane pH 6.3
Crystal Properties Matthews coefficient Solvent content 4.21 70.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.826 α = 90 b = 195.621 β = 95.85 c = 100.209 γ = 90
Symmetry Space Group P 1 21 1
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 2016-07-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.9780 APS 22-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 2.92 50 99.1 0.067 0.076 15.2 4.2 82460
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 2.92 3.09 95.3 0.9 1.05 1.8 3.9
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 2.92 39.17 81223 1237 99.15 0.198 0.197 0.1975 0.25 0.244 RANDOM 100.861
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] 1.02 0.16 -0.98 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.253 r_dihedral_angle_3_deg 16.676 r_dihedral_angle_4_deg 12.995 r_dihedral_angle_1_deg 7.07 r_long_range_B_refined 5.868 r_long_range_B_other 5.867 r_mcangle_it 3.731 r_mcangle_other 3.73 r_scangle_other 3.241 r_mcbond_it 2.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.253 r_dihedral_angle_3_deg 16.676 r_dihedral_angle_4_deg 12.995 r_dihedral_angle_1_deg 7.07 r_long_range_B_refined 5.868 r_long_range_B_other 5.867 r_mcangle_it 3.731 r_mcangle_other 3.73 r_scangle_other 3.241 r_mcbond_it 2.07 r_mcbond_other 2.07 r_scbond_it 1.761 r_scbond_other 1.761 r_angle_refined_deg 1.286 r_angle_other_deg 0.914 r_chiral_restr 0.072 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 15480 Nucleic Acid Atoms Solvent Atoms 40 Heterogen Atoms 36
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling HKL-3000 phasing