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The structure of DHAR1 from Arabidopsis thaliana
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5EL8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Protein at 20 mg/ml, 20% PEG 8000, 0.2 M NaK Phosphate, 0.1M TRIS
Crystal Properties Matthews coefficient Solvent content 3.19 61.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 63.69 α = 90 b = 63.69 β = 90 c = 266.35 γ = 120
Symmetry Space Group P 65 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 2014-05-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I24 0.979 Diamond I24
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 2.28 54.01 99.7 0.043 35.9 18.1 15525
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 2.28 2.34 99.6 0.635 5.1 19.4
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 5EL8 2.28 54.01 14717 774 99.51 0.18374 0.1816 0.1912 0.22366 0.2348 RANDOM 64.144
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] -1.49 -0.74 -1.49 4.83
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.458 r_dihedral_angle_3_deg 15.723 r_dihedral_angle_4_deg 14.885 r_long_range_B_other 7.961 r_long_range_B_refined 7.96 r_dihedral_angle_1_deg 6.386 r_scangle_other 5.578 r_mcangle_other 4.337 r_mcangle_it 4.327 r_scbond_it 3.687
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.458 r_dihedral_angle_3_deg 15.723 r_dihedral_angle_4_deg 14.885 r_long_range_B_other 7.961 r_long_range_B_refined 7.96 r_dihedral_angle_1_deg 6.386 r_scangle_other 5.578 r_mcangle_other 4.337 r_mcangle_it 4.327 r_scbond_it 3.687 r_scbond_other 3.687 r_mcbond_it 3.05 r_mcbond_other 3.018 r_angle_refined_deg 1.569 r_angle_other_deg 0.82 r_chiral_restr 0.088 r_bond_refined_d 0.012 r_gen_planes_refined 0.006 r_bond_other_d 0.002 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 1662 Nucleic Acid Atoms Solvent Atoms 89 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling