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Crystal structure of Arabidopsis thaliana HDT4
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 7.5 291 0.2 M l-proline, 0.1 m HEPES pH 7.5, 24% W/V PEG 1500
Crystal Properties Matthews coefficient Solvent content 2.15 38.66
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 90.482 α = 90 b = 73.114 β = 96.86 c = 72.58 γ = 90
Symmetry Space Group C 1 2 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 2019-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON RRCAT INDUS-2 BEAMLINE PX-BL21 0.97947 RRCAT INDUS-2 PX-BL21
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 1.85 46.29 96.9 0.997 10.9 3.7 38947
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 1.85 1.89 88.6 0.819 3.7
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 1.85 44.96 37002 1969 96.94 0.1948 0.19293 0.2051 0.22843 0.2404 RANDOM 29.881
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] 2.6 0.18 -0.98 -1.62
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.986 r_dihedral_angle_4_deg 30.753 r_dihedral_angle_3_deg 16.732 r_long_range_B_other 7.553 r_long_range_B_refined 7.545 r_dihedral_angle_1_deg 7.16 r_scangle_other 5.642 r_mcangle_it 4.169 r_mcangle_other 4.168 r_scbond_it 3.601
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.986 r_dihedral_angle_4_deg 30.753 r_dihedral_angle_3_deg 16.732 r_long_range_B_other 7.553 r_long_range_B_refined 7.545 r_dihedral_angle_1_deg 7.16 r_scangle_other 5.642 r_mcangle_it 4.169 r_mcangle_other 4.168 r_scbond_it 3.601 r_scbond_other 3.6 r_mcbond_it 2.776 r_mcbond_other 2.767 r_angle_refined_deg 1.686 r_angle_other_deg 1.083 r_chiral_restr 0.114 r_bond_refined_d 0.014 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 3903 Nucleic Acid Atoms Solvent Atoms 110 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling MOLREP phasing