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Structure and catalytic mechanism of monodehydroascorbate reductase, MDHAR, from Oryza sativa L. japonica
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4H4Q
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 295 Tris, ammonium acetate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.46 49.93
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.635 α = 90 b = 85.112 β = 90 c = 133.443 γ = 90
Symmetry Space Group P 21 21 21
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 ADSC QUANTUM 210 2015-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim 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 2.29 71.76 99.5 0.087 0.089 0.029 13 13.9 41172
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.34 100 0.502 0.699 14.9 2045
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4H4Q 2.29 50 39174 1936 99.22 0.2082 0.2055 0.2636 0.291 RANDOM 75.271
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] 3.6 -1.34 -2.25
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.848 r_dihedral_angle_3_deg 19.22 r_dihedral_angle_4_deg 17.202 r_mcangle_it 8.212 r_dihedral_angle_1_deg 7.324 r_mcbond_it 6.205 r_mcbond_other 6.204 r_angle_refined_deg 2.038 r_angle_other_deg 1.062 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.848 r_dihedral_angle_3_deg 19.22 r_dihedral_angle_4_deg 17.202 r_mcangle_it 8.212 r_dihedral_angle_1_deg 7.324 r_mcbond_it 6.205 r_mcbond_other 6.204 r_angle_refined_deg 2.038 r_angle_other_deg 1.062 r_chiral_restr 0.109 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6465 Nucleic Acid Atoms Solvent Atoms 109 Heterogen Atoms 218
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing