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Crystal structure of rice Os3BGlu7 with glucoimidazole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RGL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 288 23% PEG MME 5000, 0.17 M AMMONIUM
SULFATE, 0.1M MES, PH 6.7
Crystal Properties Matthews coefficient Solvent content 2.57 52.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 80.402 α = 90 b = 101.557 β = 90 c = 127.458 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX300HE 2016-06-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9 SPring-8 BL44XU
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 2.3 50.01 99.9 0.998 17.3 6.9 47470
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 2.3 2.34 0.947 6.6
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 2RGL 2.3 50.01 44707 2314 99.83 0.1786 0.1766 0.185 0.217 0.2232 RANDOM 30.512
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] -0.66 0.7 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.294 r_dihedral_angle_4_deg 20.632 r_dihedral_angle_3_deg 12.664 r_dihedral_angle_1_deg 6.194 r_angle_refined_deg 1.265 r_angle_other_deg 0.942 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.294 r_dihedral_angle_4_deg 20.632 r_dihedral_angle_3_deg 12.664 r_dihedral_angle_1_deg 6.194 r_angle_refined_deg 1.265 r_angle_other_deg 0.942 r_chiral_restr 0.077 r_bond_refined_d 0.008 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7602 Nucleic Acid Atoms Solvent Atoms 480 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing PDB_EXTRACT data extraction Coot model building