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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, lithium sulfate, PEG 5000 MME
Crystal Properties Matthews coefficient Solvent content 2.17 43.28
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.473 α = 90 b = 81.473 β = 90 c = 121.357 γ = 90
Symmetry Space Group P 41 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 ADSC QUANTUM 315r 2015-10-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PAL/PLS BEAMLINE 5C (4A) 0.97954 PAL/PLS 5C (4A)
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 2 50 99.7 0.145 5.7 14.1 53422
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 2 2.03 100 0.355 14.4 2673
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 4H4Q 2 50 26925 1360 99.45 0.1474 0.1444 0.1564 0.2087 0.2136 RANDOM 20.488
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] -0.21 -0.21 0.41
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.963 r_dihedral_angle_4_deg 14.685 r_dihedral_angle_3_deg 14.465 r_dihedral_angle_1_deg 6.519 r_mcangle_it 3.055 r_angle_refined_deg 2.225 r_mcbond_it 2.168 r_mcbond_other 2.166 r_angle_other_deg 1.398 r_chiral_restr 0.234
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.963 r_dihedral_angle_4_deg 14.685 r_dihedral_angle_3_deg 14.465 r_dihedral_angle_1_deg 6.519 r_mcangle_it 3.055 r_angle_refined_deg 2.225 r_mcbond_it 2.168 r_mcbond_other 2.166 r_angle_other_deg 1.398 r_chiral_restr 0.234 r_bond_refined_d 0.024 r_gen_planes_refined 0.013 r_bond_other_d 0.003 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3278 Nucleic Acid Atoms Solvent Atoms 394 Heterogen Atoms 97
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection SCALEPACK data scaling PDB_EXTRACT data extraction HKL-2000 data reduction MOLREP phasing