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Crystal Structure of Glycogen Phosphorylase DK5 complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2PRJ PDB entry 2PRJ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 SMALL TUBES 6.7 289 10MM BES BUFFER, 3MM DDT, pH 6.7, small tubes, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.5 50.75
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 129.132 α = 90 b = 129.132 β = 90 c = 117.01 γ = 90
Symmetry Space Group P 43 21 2
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 289 CCD MAR CCD 165 mm 2009-07-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON EMBL/DESY, HAMBURG BEAMLINE X13 0.81 EMBL/DESY, HAMBURG X13
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 99 97.5 0.051 4.9 5 65604 -3
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) 2 2.03 98.3 0.493 2.2 4.8 3272
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 FOURIER SYNTHESIS THROUGHOUT PDB entry 2PRJ 2 49.27 65585 3319 97.56 0.185 0.184 0.1832 0.215 0.2157 RANDOM 31.109
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] 0.03 0.03 -0.05
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.244 r_dihedral_angle_4_deg 19.797 r_dihedral_angle_3_deg 15.193 r_dihedral_angle_1_deg 5.437 r_scangle_it 2.889 r_scbond_it 1.768 r_mcangle_it 1.222 r_angle_refined_deg 1.182 r_mcbond_it 0.654 r_nbtor_refined 0.304
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.244 r_dihedral_angle_4_deg 19.797 r_dihedral_angle_3_deg 15.193 r_dihedral_angle_1_deg 5.437 r_scangle_it 2.889 r_scbond_it 1.768 r_mcangle_it 1.222 r_angle_refined_deg 1.182 r_mcbond_it 0.654 r_nbtor_refined 0.304 r_nbd_refined 0.189 r_symmetry_vdw_refined 0.147 r_symmetry_hbond_refined 0.123 r_xyhbond_nbd_refined 0.119 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.004
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6597 Nucleic Acid Atoms Solvent Atoms 293 Heterogen Atoms 26
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction DNA data collection REFMAC phasing