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Crystal Structure of ABBA+UDP+Gal at pH 9.0 with MPD as the cryoprotectant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8 298 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 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.27 45.91
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.52 α = 90 b = 149.28 β = 90 c = 79.75 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 2008-12-04 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 1.55 20 97.8 0.036 17.5 4.43 44858
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 1.55 1.61 99.5 0.319 3.3 3.7 4505
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 1LZ7 1.55 20 44856 2269 97.69 0.1799 0.1781 0.1729 0.2142 0.2097 RANDOM 25.1813
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] -0.68 0.31 0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.124 r_dihedral_angle_4_deg 19.404 r_dihedral_angle_3_deg 14.402 r_dihedral_angle_1_deg 6.685 r_angle_refined_deg 2.297 r_angle_other_deg 1.168 r_chiral_restr 0.148 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.124 r_dihedral_angle_4_deg 19.404 r_dihedral_angle_3_deg 14.402 r_dihedral_angle_1_deg 6.685 r_angle_refined_deg 2.297 r_angle_other_deg 1.168 r_chiral_restr 0.148 r_bond_refined_d 0.025 r_gen_planes_refined 0.013 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2320 Nucleic Acid Atoms Solvent Atoms 317 Heterogen Atoms 38
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