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Crystal Structure of 1,2-beta-oligoglucan phosphorylase from Lachnoclostridium phytofermentans
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 298 Tris-HCl, calcium acetate, PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.53 51.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 87.761 α = 90 b = 94.784 β = 98.41 c = 157.943 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 210r 2014-12-21 M MAD
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE BL-5A 0.97932 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 50 100 0.121 25.8 14.6 172867
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 2.03 100 0.861 2.8 14.3 8557
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 SAD THROUGHOUT 2 42.72 164157 8658 99.62 0.17019 0.16842 0.1775 0.20359 0.211 RANDOM 30.95
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.889 r_dihedral_angle_4_deg 18.603 r_dihedral_angle_3_deg 14.291 r_dihedral_angle_1_deg 6.489 r_long_range_B_refined 6.031 r_long_range_B_other 6.03 r_scangle_other 5.058 r_scbond_it 3.514 r_scbond_other 3.514 r_mcangle_it 3.39
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.889 r_dihedral_angle_4_deg 18.603 r_dihedral_angle_3_deg 14.291 r_dihedral_angle_1_deg 6.489 r_long_range_B_refined 6.031 r_long_range_B_other 6.03 r_scangle_other 5.058 r_scbond_it 3.514 r_scbond_other 3.514 r_mcangle_it 3.39 r_mcangle_other 3.39 r_mcbond_it 2.587 r_mcbond_other 2.587 r_angle_refined_deg 1.667 r_angle_other_deg 1.371 r_chiral_restr 0.113 r_bond_refined_d 0.018 r_gen_planes_refined 0.01 r_bond_other_d 0.008 r_gen_planes_other 0.005 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 17836 Nucleic Acid Atoms Solvent Atoms 871 Heterogen Atoms 84
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHENIX phasing