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The structure of AxCesD octamer complexed with cellopentaose
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Z9F PDB ENTRY 2Z9F
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.4 293 0.1M PHOSPHATE-CITRATE, 0.2M LI2SO4, 10% (V/V) ISO-PROPANOL, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.28 62.51
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 132.877 α = 90 b = 132.877 β = 90 c = 216.667 γ = 90
Symmetry Space Group I 41 2 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 MIRRORS 2007-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL41XU 1.0 SPring-8 BL41XU
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 3 50 99.9 0.088 0.088 24.067 10 19771 -3 70.456
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 3 3.11 99.9 0.399 0.399 3.41 9 1944
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 2Z9F 3 19.94 19682 1925 100 0.24677 0.24178 0.236 0.29259 0.2352 RANDOM 56.634
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] 1.05 1.05 -2.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.736 r_dihedral_angle_3_deg 22.525 r_dihedral_angle_4_deg 19.86 r_dihedral_angle_1_deg 6.934 r_angle_refined_deg 1.469 r_mcangle_it 0.885 r_scangle_it 0.872 r_mcbond_it 0.498 r_scbond_it 0.491 r_nbtor_refined 0.325
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 44.736 r_dihedral_angle_3_deg 22.525 r_dihedral_angle_4_deg 19.86 r_dihedral_angle_1_deg 6.934 r_angle_refined_deg 1.469 r_mcangle_it 0.885 r_scangle_it 0.872 r_mcbond_it 0.498 r_scbond_it 0.491 r_nbtor_refined 0.325 r_symmetry_vdw_refined 0.309 r_nbd_refined 0.277 r_xyhbond_nbd_refined 0.154 r_symmetry_hbond_refined 0.15 r_chiral_restr 0.094 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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 4828 Nucleic Acid Atoms Solvent Atoms 178 Heterogen Atoms 168
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling LAFIRE phasing