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Crystal Structure of ABBA+UDP+Gal at pH 8.0 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 45.8
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.53 α = 90 b = 149.73 β = 90 c = 79.34 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 2008-11-28 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 1.54 20 98.1 0.036 19.6 4.56 45812
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 1.54 1.6 99 0.287 3.9 3.81 4555
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 1.54 20 45812 2321 98.07 0.1824 0.1812 0.1747 0.205 0.1994 RANDOM 21.9435
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] -0.37 0.28 0.09
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.862 r_dihedral_angle_4_deg 15.429 r_dihedral_angle_3_deg 14.946 r_dihedral_angle_1_deg 6.831 r_angle_refined_deg 2.305 r_angle_other_deg 1.134 r_chiral_restr 0.137 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.001
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.862 r_dihedral_angle_4_deg 15.429 r_dihedral_angle_3_deg 14.946 r_dihedral_angle_1_deg 6.831 r_angle_refined_deg 2.305 r_angle_other_deg 1.134 r_chiral_restr 0.137 r_bond_refined_d 0.026 r_gen_planes_refined 0.012 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2312 Nucleic Acid Atoms Solvent Atoms 315 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