2QLM

Glycogen phosphorylase in complex with FN67


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES6.728910 mM Bes, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4750.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.633α = 90
b = 128.633β = 90
c = 116.545γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293IMAGE PLATEMAR scanner 345 mm plate2004-11-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X310.8123EMBL/DESY, HAMBURGX31

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
12.13093.10.08521.73.45361953619-325.3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.12.14900.4445.83.12561

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)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 DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTPDB ENTRY 2PRJ2.1305087250872272993.150.185360.185360.183820.21445RANDOM25.624
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]
0.50.5-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.236
r_dihedral_angle_4_deg18.544
r_dihedral_angle_3_deg15.191
r_dihedral_angle_1_deg5.161
r_scangle_it1.92
r_scbond_it1.155
r_angle_refined_deg1.03
r_mcangle_it0.891
r_mcbond_it0.529
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.236
r_dihedral_angle_4_deg18.544
r_dihedral_angle_3_deg15.191
r_dihedral_angle_1_deg5.161
r_scangle_it1.92
r_scbond_it1.155
r_angle_refined_deg1.03
r_mcangle_it0.891
r_mcbond_it0.529
r_nbtor_refined0.302
r_nbd_refined0.179
r_symmetry_vdw_refined0.14
r_xyhbond_nbd_refined0.107
r_symmetry_hbond_refined0.086
r_chiral_restr0.074
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6603
Nucleic Acid Atoms
Solvent Atoms286
Heterogen Atoms24

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling