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Crystal structure of Galacto-N-biose/Lacto-N-biose I phosphorylase in complex with GalNAc
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 6.5 277 Na cacodyrate, Mg(NO3)2, PEG 4000, GalNAc, pH 6.5, VAPOR DIFFUSION, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.41 49.01
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.861 α = 105.2 b = 111.658 β = 90.48 c = 118.66 γ = 107.27
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 4 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 BL-17A 1.000 Photon Factory BL-17A 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 1.9 50 97 0.057 21.066 2.6 640661 243435 23.6
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 1.9 1.97 96 0.232 3.5 2.6 24136
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 MOLECULAR REPLACEMENT THROUGHOUT 1.9 44.81 243428 12254 96.7 0.163 0.161 0.1613 0.204 0.2051 RANDOM 28.094
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 0.07 0.03 0.08 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.223 r_dihedral_angle_4_deg 17.628 r_dihedral_angle_3_deg 13.579 r_dihedral_angle_1_deg 5.9 r_scangle_it 3.083 r_scbond_it 1.993 r_angle_refined_deg 1.368 r_mcangle_it 1.24 r_mcbond_it 0.704 r_chiral_restr 0.102
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.223 r_dihedral_angle_4_deg 17.628 r_dihedral_angle_3_deg 13.579 r_dihedral_angle_1_deg 5.9 r_scangle_it 3.083 r_scbond_it 1.993 r_angle_refined_deg 1.368 r_mcangle_it 1.24 r_mcbond_it 0.704 r_chiral_restr 0.102 r_bond_refined_d 0.014 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 23573 Nucleic Acid Atoms Solvent Atoms 3114 Heterogen Atoms 124
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