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The crystal structure of rice (Oryza sativa L.) Os4BGlu12 with dinitrophenyl 2-deoxy-2-fluoro-beta-D-glucopyranoside
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Native Os4BGlu12
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 288.15 19% PEG 2000, 0.1M Tris HCl, 0.16M NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.15K
Crystal Properties Matthews coefficient Solvent content 2.62 53.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 114.112 α = 90 b = 114.112 β = 90 c = 184.541 γ = 90
Symmetry Space Group P 43 21 2
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 ADSC QUANTUM 315 2008-06-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL13B1 1.0000 NSRRC BL13B1
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 2.45 30 99.9 0.094 4.4 8.6 43131
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 2.45 2.51 99.9 0.49 4.4 8.6 381316
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 Native Os4BGlu12 2.45 30 43131 2292 99.81 0.21113 0.20903 0.2072 0.25065 0.2519 RANDOM 33.562
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] 0.51 0.51 -1.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.384 r_dihedral_angle_4_deg 20.182 r_dihedral_angle_3_deg 17.585 r_dihedral_angle_1_deg 7.509 r_mcangle_it 2.145 r_scangle_it 1.885 r_mcbond_it 1.831 r_angle_refined_deg 1.264 r_scbond_it 1.162 r_nbtor_refined 0.312
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.384 r_dihedral_angle_4_deg 20.182 r_dihedral_angle_3_deg 17.585 r_dihedral_angle_1_deg 7.509 r_mcangle_it 2.145 r_scangle_it 1.885 r_mcbond_it 1.831 r_angle_refined_deg 1.264 r_scbond_it 1.162 r_nbtor_refined 0.312 r_nbd_refined 0.207 r_symmetry_vdw_refined 0.175 r_xyhbond_nbd_refined 0.155 r_symmetry_hbond_refined 0.151 r_metal_ion_refined 0.105 r_chiral_restr 0.093 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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_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 7722 Nucleic Acid Atoms Solvent Atoms 280 Heterogen Atoms 79
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling