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Crystal structure of BBBB+UDP+Gal with MPD as the cryoprotectant
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LZ7 PDB ENTRY 1LZ7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 298 1% PEG4000, 5% MPD, 100 mM ammonium sulfate, 70 mM sodium chloride, 50 mM ADA, pH 7.6, 30 mM sodium acetate, pH 4.6, 5 mM manganese chloride, with 20% MPD as cryoprotectant, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.28 45.96
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.56 α = 90 b = 149.83 β = 90 c = 78.97 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 2007-12-14 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 74.953 96.9 0.055 13.5 4.37 44205
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 94.7 0.429 3 3.75 4248
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1LZ7 1.55 20 44203 2229 96.89 0.1929 0.191 0.2271 0.2121 RANDOM 23.6228
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] -0.35 0.4 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.263 r_dihedral_angle_4_deg 22.887 r_dihedral_angle_3_deg 14.867 r_dihedral_angle_1_deg 6.699 r_scangle_it 5.446 r_scbond_it 3.638 r_mcangle_it 2.305 r_angle_refined_deg 2.267 r_mcbond_it 1.457 r_chiral_restr 0.168
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.263 r_dihedral_angle_4_deg 22.887 r_dihedral_angle_3_deg 14.867 r_dihedral_angle_1_deg 6.699 r_scangle_it 5.446 r_scbond_it 3.638 r_mcangle_it 2.305 r_angle_refined_deg 2.267 r_mcbond_it 1.457 r_chiral_restr 0.168 r_bond_refined_d 0.028 r_gen_planes_refined 0.014
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2225 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 45
Software Software Software Name Purpose d*TREK data reduction REFMAC refinement PDB_EXTRACT data extraction CrystalClear data collection d*TREK data scaling MOLREP phasing