3MRX

Glycogen phosphorylase complexed with 4-methoxybenzaldehyde-4-(2,3,4,6-tetra-O-acetyl-beta-D-glucopyranosyl)-thiosemicarbazone


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2PRJPDB ENTRY 2PRJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES6.728920 mg/ml of protein in a buffer solution containing 10 mM BES pH 6.7, 1 mM EDTA and 3 mM DTT. 6.7mM inhibitor in 20% DMSO soaked with native crystals for 3 hrs, SMALL TUBES, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4549.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.31α = 90
b = 128.31β = 90
c = 116.05γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDMARMOSAIC 225 mm CCD2007-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.11.04498SRSPX10.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (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
11.9535.5897.80.0718.356903269032-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.952.0697.20.36654.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2PRJ1.9531.1165522349097.360.183670.181970.21606RANDOM29.839
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]
0.050.05-0.11
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.093
r_dihedral_angle_4_deg19.727
r_dihedral_angle_3_deg15.636
r_dihedral_angle_1_deg5.472
r_scangle_it3.113
r_scbond_it1.826
r_mcangle_it1.231
r_angle_refined_deg1.15
r_mcbond_it0.632
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.093
r_dihedral_angle_4_deg19.727
r_dihedral_angle_3_deg15.636
r_dihedral_angle_1_deg5.472
r_scangle_it3.113
r_scbond_it1.826
r_mcangle_it1.231
r_angle_refined_deg1.15
r_mcbond_it0.632
r_nbtor_refined0.304
r_nbd_refined0.181
r_symmetry_vdw_refined0.144
r_symmetry_hbond_refined0.104
r_xyhbond_nbd_refined0.098
r_chiral_restr0.086
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6608
Nucleic Acid Atoms
Solvent Atoms324
Heterogen Atoms50

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
HKL-3000data collection
DENZOdata reduction
SCALEPACKdata scaling
CNSphasing