2QNB

Glycogen Phosphorylase b in complex with N-benzoyl-N'-beta-D-glucopyranosyl urea


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
2.4850.34

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.653α = 90
b = 128.653β = 90
c = 116.75γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDADSC QUANTUM 42001-03-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.60.87SRSPX9.6

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
11.83097.70.03815.634.98881188811-3
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)
1.81.83950.4811.944.2

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 2PRJ1.83084369444897.610.19960.198530.22025RANDOM28.684
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]
0.710.71-1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.101
r_dihedral_angle_4_deg18.738
r_dihedral_angle_3_deg15.627
r_dihedral_angle_1_deg5.01
r_scangle_it1.896
r_scbond_it1.171
r_angle_refined_deg1.025
r_mcangle_it0.856
r_mcbond_it0.499
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.101
r_dihedral_angle_4_deg18.738
r_dihedral_angle_3_deg15.627
r_dihedral_angle_1_deg5.01
r_scangle_it1.896
r_scbond_it1.171
r_angle_refined_deg1.025
r_mcangle_it0.856
r_mcbond_it0.499
r_nbtor_refined0.302
r_nbd_refined0.181
r_symmetry_vdw_refined0.116
r_symmetry_hbond_refined0.086
r_xyhbond_nbd_refined0.085
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6613
Nucleic Acid Atoms
Solvent Atoms345
Heterogen Atoms46

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling