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The Structure of variant R369A of the Mo-insertase domain Cnx1E from Arabidopsis thaliana in complex with AMP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5G2R
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293 0.1 M imidazole, 0.1 M MES pH 6.5; 0.06 M sodium nitrate, 0.06 M sodium phosphate, 0.06 M ammonium sulfate; 20 % (v/v) PEG 500 MME, 10 % PEG 8000
Crystal Properties Matthews coefficient Solvent content 2.64 53.52
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.03 α = 90 b = 123.97 β = 90 c = 132.68 γ = 90
Symmetry Space Group I 2 2 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 PIXEL DECTRIS PILATUS 6M mirrors 2017-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON BESSY BEAMLINE 14.1 0.91840 BESSY 14.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) 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 1.712 66.34 71.7 0.042 0.054 0.034 0.999 16.9 4.4 42230 -3 28.63
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.712 1.849 17.7 0.77 1.022 0.665 0.615 1.5 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 5G2R 1.712 25.07 42206 2121 71.6 0.174 0.173 0.1742 0.199 0.2088 RANDOM 33.22
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] -0.0848 0.9342 -0.8494
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.1 t_omega_torsion 3.71 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.1 t_omega_torsion 3.71 t_angle_deg 1.07 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_chiral_improper_torsion t_sum_occupancies t_utility_distance t_utility_angle t_utility_torsion t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3083 Nucleic Acid Atoms Solvent Atoms 396 Heterogen Atoms 51
Software Software Software Name Purpose BUSTER refinement XDS data reduction STARANISO data scaling PHASER phasing Coot model building autoBUSTER refinement