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Crystal structure of Arabidopsis thaliana HDT3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 7VMF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 291 0.1 M succinic acid pH 7.0, 0.1 M bicine, 30% V/V PEG MME 550
Crystal Properties Matthews coefficient Solvent content 2.18 43.69
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 54.623 α = 90 b = 77.6 β = 91.82 c = 55.511 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 CCD MARMOSAIC 225 mm CCD 2019-09-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.979470 RRCAT INDUS-2 PX-BL21
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) 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 1.75 45.13 99.5 0.037 0.051 0.999 16.9 3.9 46503
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.78 99.8 0.495 0.678 0.869 2.3 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 7VMF 1.8 35.26 40545 2164 99.4 0.191 0.19 0.1993 0.211 0.2195 RANDOM 40.76
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] -4.63 -0.41 7.64 -2.98
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.826 r_dihedral_angle_4_deg 20.523 r_dihedral_angle_3_deg 15.729 r_dihedral_angle_1_deg 8.091 r_long_range_B_other 6.099 r_long_range_B_refined 6.095 r_scangle_other 3.168 r_mcangle_it 2.783 r_mcangle_other 2.782 r_scbond_it 2.054
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.826 r_dihedral_angle_4_deg 20.523 r_dihedral_angle_3_deg 15.729 r_dihedral_angle_1_deg 8.091 r_long_range_B_other 6.099 r_long_range_B_refined 6.095 r_scangle_other 3.168 r_mcangle_it 2.783 r_mcangle_other 2.782 r_scbond_it 2.054 r_scbond_other 2.054 r_angle_refined_deg 1.759 r_mcbond_it 1.672 r_mcbond_other 1.665 r_angle_other_deg 1.103 r_chiral_restr 0.113 r_bond_refined_d 0.015 r_gen_planes_refined 0.008 r_bond_other_d 0.001 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 3801 Nucleic Acid Atoms Solvent Atoms 116 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing