☰ Navigation Tabs
Crystal structure of b-1,4-mannopyranosyl-chitobiose phosphorylase at 1.60 Angstrom in complex with N-acetylglucosamine and inorganic phosphate
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1VKD PDB ENTRY 1VKD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7 PROTEIN WAS CRYSTALLIZED FROM 17.5% PEG 3350, 200 MM NH4CL, PH 7.0
Crystal Properties Matthews coefficient Solvent content 2.11 41.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.816 α = 90 b = 140.912 β = 90 c = 168.598 γ = 90
Symmetry Space Group P 21 21 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 PIXEL DECTRIS PILATUS 6M PAIR OF KB MIRRORS FOR ADJUSTABLE FOCUSING 2014-09-26 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC ALBA XALOC
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 1.6 47 99.9 0.1 14.49 9.37 261651 -1
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 1.6 1.7 99.3 1.1 2.07 9.4
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 PDB ENTRY 1VKD 1.6 108.12 248496 13154 99.84 0.15507 0.15361 0.1681 0.18297 0.1937 RANDOM 22.301
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 -0.56 0.52
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.883 r_dihedral_angle_4_deg 14.252 r_dihedral_angle_3_deg 12.736 r_dihedral_angle_1_deg 6.968 r_long_range_B_refined 5.35 r_long_range_B_other 5.347 r_scangle_other 3.71 r_scbond_it 2.479 r_scbond_other 2.479 r_mcangle_it 2.212
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.883 r_dihedral_angle_4_deg 14.252 r_dihedral_angle_3_deg 12.736 r_dihedral_angle_1_deg 6.968 r_long_range_B_refined 5.35 r_long_range_B_other 5.347 r_scangle_other 3.71 r_scbond_it 2.479 r_scbond_other 2.479 r_mcangle_it 2.212 r_mcangle_other 2.212 r_angle_refined_deg 1.89 r_mcbond_it 1.519 r_mcbond_other 1.518 r_angle_other_deg 0.919 r_chiral_restr 0.129 r_bond_refined_d 0.019 r_gen_planes_refined 0.011 r_bond_other_d 0.001 r_gen_planes_other 0.001 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 15410 Nucleic Acid Atoms Solvent Atoms 1463 Heterogen Atoms 188
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing