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Crystal Structure of Rice GID1 complexed with GA4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 293 15% PEG4000, 8% MPD, 0.2M NaNO3, 0.1M HEPES pH7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.59 52.57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 82.76 α = 90 b = 133.895 β = 104.95 c = 118.886 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 90 CCD ASDC QUANTUM 210 2008-06-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0000 SPring-8 BL41XU
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 1.9 50 98.8 0.054 21.8 3.6 193933
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 1.9 1.97 92.8 0.597 3.4 18231
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 SAD THROUGHOUT 1.9 20 183960 9761 100 0.2026 0.20044 0.2024 0.24369 0.245 RANDOM 34.444
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] -0.06 -2.53 0.36 -1.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.682 r_dihedral_angle_4_deg 16.973 r_dihedral_angle_3_deg 14.117 r_dihedral_angle_1_deg 6.006 r_scangle_it 3.188 r_scbond_it 2.211 r_mcangle_it 1.569 r_angle_refined_deg 1.507 r_mcbond_it 0.928 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.682 r_dihedral_angle_4_deg 16.973 r_dihedral_angle_3_deg 14.117 r_dihedral_angle_1_deg 6.006 r_scangle_it 3.188 r_scbond_it 2.211 r_mcangle_it 1.569 r_angle_refined_deg 1.507 r_mcbond_it 0.928 r_nbtor_refined 0.312 r_nbd_refined 0.2 r_xyhbond_nbd_refined 0.137 r_symmetry_vdw_refined 0.129 r_chiral_restr 0.096 r_symmetry_hbond_refined 0.082 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14549 Nucleic Acid Atoms Solvent Atoms 1133 Heterogen Atoms 274
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing