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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 1K0O
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 Protein at 20mg/ml concentration
20% PEG 8000, 0.2M NaK Phosphate, 0.1M Tris
Crystal Properties Matthews coefficient Solvent content 3.19 61.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.9 α = 90 b = 64.9 β = 90 c = 259 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-F 2014-03-08 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I02 0.979 Diamond I02
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 2.3 56.2 99.9 0.132 6.1 5.4 15743
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 2.35 99.8 0.8 1 5.3
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 1K0O 2.3 56.2 14573 711 99.82 0.20505 0.20346 0.2043 0.23616 0.2381 RANDOM 67.776
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] -0.68 -0.34 -0.68 2.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.667 r_dihedral_angle_3_deg 17.059 r_long_range_B_refined 7.203 r_dihedral_angle_1_deg 6.352 r_mcangle_it 3.264 r_scbond_it 2.858 r_mcbond_it 2.258 r_dihedral_angle_4_deg 1.815 r_angle_refined_deg 1.593 r_chiral_restr 0.103
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.667 r_dihedral_angle_3_deg 17.059 r_long_range_B_refined 7.203 r_dihedral_angle_1_deg 6.352 r_mcangle_it 3.264 r_scbond_it 2.858 r_mcbond_it 2.258 r_dihedral_angle_4_deg 1.815 r_angle_refined_deg 1.593 r_chiral_restr 0.103 r_bond_refined_d 0.012 r_gen_planes_refined 0.007 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_mcangle_other r_scbond_other r_scangle_it r_scangle_other r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1666 Nucleic Acid Atoms Solvent Atoms 57 Heterogen Atoms 6
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing