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The crystal structure of rice (Oryza sativa L.) Os4BGlu12
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CBG PDB ENTRY 1CBG
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 288.15 19% PEG 3350, 0.1M Tris HCl, 0.16M NaCl, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 288.15K
Crystal Properties Matthews coefficient Solvent content 2.53 51.44
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 112.656 α = 90 b = 112.656 β = 90 c = 182.773 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 2.49 30 99.9 0.106 6.4 10 39535
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 2.5 2.59 99.9 0.41 6.4 9.7
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 PDB ENTRY 1CBG 2.49 30 39535 2097 99.82 0.20472 0.20245 0.2019 0.24764 0.2475 RANDOM 32.956
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] 1.07 1.07 -2.13
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.736 r_dihedral_angle_4_deg 19.477 r_dihedral_angle_3_deg 16.897 r_dihedral_angle_1_deg 5.907 r_scangle_it 2.129 r_scbond_it 1.32 r_angle_refined_deg 1.192 r_mcangle_it 0.963 r_mcbond_it 0.526 r_nbtor_refined 0.311
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.736 r_dihedral_angle_4_deg 19.477 r_dihedral_angle_3_deg 16.897 r_dihedral_angle_1_deg 5.907 r_scangle_it 2.129 r_scbond_it 1.32 r_angle_refined_deg 1.192 r_mcangle_it 0.963 r_mcbond_it 0.526 r_nbtor_refined 0.311 r_symmetry_vdw_refined 0.214 r_nbd_refined 0.202 r_xyhbond_nbd_refined 0.154 r_metal_ion_refined 0.12 r_chiral_restr 0.092 r_symmetry_hbond_refined 0.084 r_bond_refined_d 0.009 r_gen_planes_refined 0.004 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 231 Heterogen Atoms 17
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling