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Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GlcNAc and sulfate
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 6.5 277 Na cacodyrate, Mg(NO3)2, PEG 4000, GlcNAc, MgSO4, pH 6.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.42 49.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.905 α = 105.21 b = 112.039 β = 90.43 c = 118.662 γ = 107.32
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 2007-03-11 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 2.1 50 98.2 0.089 15.936 4 180455
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 2.1 2.18 97.1 0.327 2.8 4
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method 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 MAD THROUGHOUT 2.11 41.07 170072 8997 97.36 0.17184 0.16906 0.1692 0.22479 0.2242 RANDOM 25.986
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] 0.04 0.03 -0.02 -0.05 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.11 r_dihedral_angle_4_deg 17.526 r_dihedral_angle_3_deg 14.243 r_dihedral_angle_1_deg 5.944 r_scangle_it 2.934 r_scbond_it 1.856 r_angle_refined_deg 1.3 r_mcangle_it 1.137 r_mcbond_it 0.637 r_chiral_restr 0.095
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.11 r_dihedral_angle_4_deg 17.526 r_dihedral_angle_3_deg 14.243 r_dihedral_angle_1_deg 5.944 r_scangle_it 2.934 r_scbond_it 1.856 r_angle_refined_deg 1.3 r_mcangle_it 1.137 r_mcbond_it 0.637 r_chiral_restr 0.095 r_bond_refined_d 0.036 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23395 Nucleic Acid Atoms Solvent Atoms 2281 Heterogen Atoms 106
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 SHARP phasing