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Structure of rabbit muscle glycogen phosphorylase in complex with thienopyrrole
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other IN HOUSE MODEL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.7 289 1.1mM IMP
1.1mM Spermin
10mM BES
2.9mM DTT
0.1mM EDTA, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties Matthews coefficient Solvent content 2.43 49.32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 126.781 α = 90 b = 126.781 β = 90 c = 115.144 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 100 CCD ADSC QUANTUM 4 Toroidal Zerodur mirror 2001-10-07 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 0.93 ESRF ID14-4
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.3 91.29 98.34 40113 39447 1
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.54 39.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (I) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT IN HOUSE MODEL 2.3 91.29 1 40113 39447 2093 98.34 0.18564 0.18564 0.18249 0.2451 0.2611 RANDOM 29.819
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] 1.3 1.3 -2.6
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.39 r_dihedral_angle_4_deg 20.133 r_dihedral_angle_3_deg 18.051 r_dihedral_angle_1_deg 6.784 r_scangle_it 2.754 r_scbond_it 1.889 r_angle_refined_deg 1.566 r_mcangle_it 1.141 r_angle_other_deg 1.14 r_mcbond_it 0.957
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.39 r_dihedral_angle_4_deg 20.133 r_dihedral_angle_3_deg 18.051 r_dihedral_angle_1_deg 6.784 r_scangle_it 2.754 r_scbond_it 1.889 r_angle_refined_deg 1.566 r_mcangle_it 1.141 r_angle_other_deg 1.14 r_mcbond_it 0.957 r_symmetry_vdw_other 0.256 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.211 r_nbd_other 0.19 r_nbtor_refined 0.181 r_symmetry_hbond_refined 0.173 r_xyhbond_nbd_refined 0.171 r_mcbond_other 0.165 r_chiral_restr 0.09 r_nbtor_other 0.089 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6545 Nucleic Acid Atoms Solvent Atoms 455 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement ADSC data collection MOSFLM data reduction AMoRE phasing