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Crystal structure of Raucaffricine glucosidase from ajmaline biosynthesis pathway
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2JF7 PDB ENTRY 2JF7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 0.01 TO 0.3 M AMMONIUM SULFATE, 0.1 M SODIUM ACETATE, PH 4.5 TO 5.0, 9 TO 12% (W/V) PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.9 57
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 102.774 α = 90 b = 127.329 β = 90 c = 215.837 γ = 90
Symmetry Space Group I 2 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 IMAGE PLATE MAR555 FLAT PANEL MIRROR 2006-05-18 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X11 EMBL/DESY, HAMBURG X11
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 2.15 20 99.3 0.12 24.6 15.3 76299 2 32
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 2.15 2.3 98.8 0.69 4.4 15
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 2JF7 2.15 19.99 75240 1054 99.26 0.16593 0.16541 0.1777 0.20355 0.2151 RANDOM 36.186
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] -0.12 0.1 0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.565 r_dihedral_angle_4_deg 20.364 r_dihedral_angle_3_deg 14.597 r_dihedral_angle_1_deg 6.241 r_scangle_it 3.219 r_scbond_it 2.52 r_angle_refined_deg 1.689 r_mcangle_it 1.137 r_mcbond_it 0.69 r_chiral_restr 0.117
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.565 r_dihedral_angle_4_deg 20.364 r_dihedral_angle_3_deg 14.597 r_dihedral_angle_1_deg 6.241 r_scangle_it 3.219 r_scbond_it 2.52 r_angle_refined_deg 1.689 r_mcangle_it 1.137 r_mcbond_it 0.69 r_chiral_restr 0.117 r_bond_refined_d 0.023 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7510 Nucleic Acid Atoms Solvent Atoms 443 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling Auto-Rickshaw phasing