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Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc, Ethylene glycol, and nitrate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Identical protein belonging to different space group
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 277 Na cacodyrate, Mg(NO3)2, PEG 4000, GlcNAc, pH 6.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.23 44.83
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 204.043 α = 90 b = 68.02 β = 108.79 c = 116.047 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 95 CCD ADSC QUANTUM 210 2007-06-04 M SINGLE WAVELENGTH 2 1 x-ray 100 CCD ADSC QUANTUM 315 2006-11-29 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.000 Photon Factory AR-NW12A 2 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97934, 0.97974, 0.96450 Photon Factory BL-5A
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 1.85 50 98.5 0.068 21.811 3.8 126352 19.7
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) 1.85 1.92 97.7 0.25 2.7 3.9 12453
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 Identical protein belonging to different space group 1.85 35.14 126337 6359 98.37 0.151 0.149 0.1492 0.192 0.1933 RANDOM 22.142
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] -0.01 0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.016 r_dihedral_angle_4_deg 18.325 r_dihedral_angle_3_deg 12.587 r_dihedral_angle_1_deg 5.821 r_scangle_it 3.242 r_scbond_it 2.044 r_angle_refined_deg 1.325 r_mcangle_it 1.287 r_mcbond_it 0.724 r_chiral_restr 0.098
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.016 r_dihedral_angle_4_deg 18.325 r_dihedral_angle_3_deg 12.587 r_dihedral_angle_1_deg 5.821 r_scangle_it 3.242 r_scbond_it 2.044 r_angle_refined_deg 1.325 r_mcangle_it 1.287 r_mcbond_it 0.724 r_chiral_restr 0.098 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11787 Nucleic Acid Atoms Solvent Atoms 1826 Heterogen Atoms 94
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing