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Crystal structure of Pennisetum glaucum monodehydroascorbate reductase in complex with FADH2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5JCI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293.15 0.2 M Sodium acetate trihydrate
0.1 M Sodium cacodylate trihydrate pH 6.5
30% w/v Polyethylene glycol 8,000
Crystal Properties Matthews coefficient Solvent content 2.19 45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 65.73 α = 96.39 b = 79.118 β = 97.27 c = 90.687 γ = 111.92
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 345 mm plate 2019-01-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 2.37 61.45 96.6 0.997 2.21 4.9 64802
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.373 2.413 0.997
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 5JCI 2.373 61.45 64801 3231 96.6 0.1886 0.1857 0.1803 0.2432 0.2334 RANDOM 41.01
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] 5.5957 2.761 -5.1746 5.9714 -1.7536 -11.5671
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.88 t_omega_torsion 3.17 t_angle_deg 0.98 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 16.88 t_omega_torsion 3.17 t_angle_deg 0.98 t_bond_d 0.008 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion t_pseud_angle 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 12847 Nucleic Acid Atoms Solvent Atoms 553 Heterogen Atoms 388
Software Software Software Name Purpose BUSTER refinement PDB_EXTRACT data extraction ARP/wARP model building BALBES phasing PHENIX model building autoPROC data reduction autoPROC data scaling