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Crystal structure of Arabidopsis thaliana HDT2
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 6J2Z
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 0.2M ammonium phosphate dibasic pH-8.0, 20%W/V PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.44 49.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 53.106 α = 90 b = 96.221 β = 90 c = 196.299 γ = 90
Symmetry Space Group C 2 2 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 103 PIXEL DECTRIS PILATUS 6M 2017-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 1.07227 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) 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 1.32 49.07 95 0.999 13.9 3.6 111734
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.32 1.34 77.2 0.853 2.1 2.4
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 6J2Z 1.32 46.77 106115 5549 94.59 0.1616 0.16015 0.1599 0.18915 0.1889 RANDOM 22.148
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] -0.74 0.5 0.24
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.115 r_dihedral_angle_3_deg 10.836 r_dihedral_angle_1_deg 6.926 r_long_range_B_refined 3.651 r_long_range_B_other 3.628 r_scangle_other 3.37 r_rigid_bond_restr 3.228 r_scbond_it 2.79 r_scbond_other 2.789 r_mcangle_it 2.536
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.115 r_dihedral_angle_3_deg 10.836 r_dihedral_angle_1_deg 6.926 r_long_range_B_refined 3.651 r_long_range_B_other 3.628 r_scangle_other 3.37 r_rigid_bond_restr 3.228 r_scbond_it 2.79 r_scbond_other 2.789 r_mcangle_it 2.536 r_mcangle_other 2.536 r_mcbond_it 1.969 r_mcbond_other 1.968 r_angle_refined_deg 1.71 r_angle_other_deg 1.053 r_chiral_restr 0.118 r_bond_refined_d 0.017 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3613 Nucleic Acid Atoms Solvent Atoms 330 Heterogen Atoms 1
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing