☰ Navigation Tabs
Crystal Structure of AAAA+UDP+Gal at pH 5.0 with MPD as the cryoprotectant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZ0
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 298 1% PEG 4000, 5% MPD, 5 mM manganese chloride, 100 mM ammonium sulfate, 70 mM sodium chloride,50 mM ADA, 30 mM sodium acetate with 20% MPD as cryoprotectant, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.7
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.3 α = 90 b = 149.22 β = 90 c = 79.36 γ = 90
Symmetry Space Group C 2 2 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 IMAGE PLATE RIGAKU RAXIS OSMIC BLUE MIRRORS 2008-12-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-002 1.54
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 2.02 20 86 0.047 15.1 3.96 17878
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 2.02 2.09 82.4 0.302 3.6 3.56
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 1LZ0 2.02 20 16954 921 85.82 0.1947 0.19145 0.187 0.25846 0.2497 RANDOM 31.77
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] 0.11 -1.08 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.384 r_dihedral_angle_4_deg 17.209 r_dihedral_angle_3_deg 17.178 r_dihedral_angle_1_deg 7.242 r_angle_refined_deg 1.88 r_angle_other_deg 1.061 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.384 r_dihedral_angle_4_deg 17.209 r_dihedral_angle_3_deg 17.178 r_dihedral_angle_1_deg 7.242 r_angle_refined_deg 1.88 r_angle_other_deg 1.061 r_chiral_restr 0.114 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 2218 Nucleic Acid Atoms Solvent Atoms 125 Heterogen Atoms 50
Software Software Software Name Purpose d*TREK data reduction PHASER phasing REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection CrystalClear data reduction d*TREK data scaling