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Structure of plastidial phosphorylase Pho1 from Barley
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZB2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.6 288 0.1M Na Citrate
30% PEG 4000
Crystal Properties Matthews coefficient Solvent content 2.31 46.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 229.21 α = 90 b = 63.48 β = 115.21 c = 148.82 γ = 90
Symmetry Space Group C 1 2 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 PIXEL DECTRIS PILATUS 6M 2013-07-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 0.95373 ESRF ID29
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.7 50 99 0.143 0.996 8.8 4.5 51731
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.7 2.9 99.1 1.1144 0.666 1.3 4.6
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 2ZB2 2.7 50 51731 1600 99.37 0.21824 0.21704 0.2233 0.25732 0.2615 RANDOM 63.261
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] 1.67 0.05 -2.64 0.65
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.736 r_dihedral_angle_4_deg 17.267 r_dihedral_angle_3_deg 16.615 r_dihedral_angle_1_deg 5.483 r_long_range_B_refined 3.401 r_long_range_B_other 3.401 r_mcangle_it 1.215 r_mcangle_other 1.215 r_scangle_other 1.034 r_angle_refined_deg 0.97
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.736 r_dihedral_angle_4_deg 17.267 r_dihedral_angle_3_deg 16.615 r_dihedral_angle_1_deg 5.483 r_long_range_B_refined 3.401 r_long_range_B_other 3.401 r_mcangle_it 1.215 r_mcangle_other 1.215 r_scangle_other 1.034 r_angle_refined_deg 0.97 r_angle_other_deg 0.701 r_mcbond_it 0.685 r_mcbond_other 0.685 r_scbond_it 0.584 r_scbond_other 0.583 r_chiral_restr 0.054 r_bond_refined_d 0.005 r_gen_planes_refined 0.003 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 13430 Nucleic Acid Atoms Solvent Atoms 148 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling PHASER phasing