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Crystal Structure of Rice GID1 complexed with GA3
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3EBL PDB ENTRY 3EBL
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 = 82.717 α = 90 b = 134.142 β = 105.2 c = 118.872 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 RAYONIX MX225HE 2008-07-18 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 97.6 0.054 27.585 3.7 192246
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 87.5 0.365 3.3 17227
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 PDB ENTRY 3EBL 1.9 20 181950 9618 100 0.19925 0.19716 0.1987 0.23946 0.2418 RANDOM 31.091
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] 0.16 -2.51 0.06 -1.54
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.588 r_dihedral_angle_4_deg 17.09 r_dihedral_angle_3_deg 13.702 r_dihedral_angle_1_deg 5.979 r_scangle_it 3.049 r_scbond_it 2.102 r_mcangle_it 1.496 r_angle_refined_deg 1.488 r_mcbond_it 0.891 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.588 r_dihedral_angle_4_deg 17.09 r_dihedral_angle_3_deg 13.702 r_dihedral_angle_1_deg 5.979 r_scangle_it 3.049 r_scbond_it 2.102 r_mcangle_it 1.496 r_angle_refined_deg 1.488 r_mcbond_it 0.891 r_nbtor_refined 0.312 r_nbd_refined 0.199 r_xyhbond_nbd_refined 0.13 r_symmetry_hbond_refined 0.116 r_chiral_restr 0.093 r_symmetry_vdw_refined 0.081 r_bond_refined_d 0.013 r_gen_planes_refined 0.006
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 14510 Nucleic Acid Atoms Solvent Atoms 1106 Heterogen Atoms 256
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 REFMAC phasing