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Arabidopsis thaliana Cytosolic Alpha-1,4-glucan Phosphorylase (PHS2)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1GPB PDB ENTRY 1GPB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.25 293 CRYSTALLISED FROM APPROXIMATELY 20% PEG3350, 100 MM AMMONIUM CITRATE PH 8.25, 10% GLYCEROL USING THE HANGING DROP VAPOUR DIFFUSION METHOD AT 20 DEG C. 1 MICROLITRE OF PROTEIN AT 10 MG PER ML IN 12.5 MM HEPES PH 7.5, 25 MM NACL WAS MIXED WITH 1 MICROLITRE OF THE WELL SOLUTION TO GIVE THE FINAL DROP
Crystal Properties Matthews coefficient Solvent content 2.26 45.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 84.67 α = 90 b = 117.1 β = 106.72 c = 94.18 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 315 2010-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 Diamond I03
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 1.7 49.11 98.9 0.08 11.8 4.2 190517 17.8
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 1.7 1.79 93.5 0.43 2.5 3.2
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 1GPB 1.7 90.2 180900 9587 98.86 0.15427 0.15278 0.1614 0.18274 0.1901 RANDOM 19.2
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] 0.25 0.06 0.16 -0.37
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.059 r_dihedral_angle_4_deg 20.519 r_dihedral_angle_3_deg 11.856 r_dihedral_angle_1_deg 5.748 r_angle_refined_deg 1.486 r_angle_other_deg 1.055 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.004
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.059 r_dihedral_angle_4_deg 20.519 r_dihedral_angle_3_deg 11.856 r_dihedral_angle_1_deg 5.748 r_angle_refined_deg 1.486 r_angle_other_deg 1.055 r_chiral_restr 0.09 r_bond_refined_d 0.013 r_gen_planes_refined 0.008 r_bond_other_d 0.004 r_gen_planes_other 0.003 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_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 13065 Nucleic Acid Atoms Solvent Atoms 1844 Heterogen Atoms 79
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing