2GM9

Structure of rabbit muscle glycogen phosphorylase in complex with thienopyrrole


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
otherIN HOUSE MODEL

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.72891.1mM IMP 1.1mM Spermin 10mM BES 2.9mM DTT 0.1mM EDTA, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4349.32

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 126.781α = 90
b = 126.781β = 90
c = 115.144γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4Toroidal Zerodur mirror2001-10-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-40.93ESRFID14-4

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.391.2998.3440113394471
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.5439.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTIN HOUSE MODEL2.391.2914011339447209398.340.185640.185640.182490.2451RANDOM29.819
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]
1.31.3-2.6
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.39
r_dihedral_angle_4_deg20.133
r_dihedral_angle_3_deg18.051
r_dihedral_angle_1_deg6.784
r_scangle_it2.754
r_scbond_it1.889
r_angle_refined_deg1.566
r_mcangle_it1.141
r_angle_other_deg1.14
r_mcbond_it0.957
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.39
r_dihedral_angle_4_deg20.133
r_dihedral_angle_3_deg18.051
r_dihedral_angle_1_deg6.784
r_scangle_it2.754
r_scbond_it1.889
r_angle_refined_deg1.566
r_mcangle_it1.141
r_angle_other_deg1.14
r_mcbond_it0.957
r_symmetry_vdw_other0.256
r_nbd_refined0.211
r_symmetry_vdw_refined0.211
r_nbd_other0.19
r_nbtor_refined0.181
r_symmetry_hbond_refined0.173
r_xyhbond_nbd_refined0.171
r_mcbond_other0.165
r_chiral_restr0.09
r_nbtor_other0.089
r_bond_refined_d0.016
r_gen_planes_refined0.006
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6545
Nucleic Acid Atoms
Solvent Atoms455
Heterogen Atoms38

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
MOSFLMdata reduction
AMoREphasing