3BCR

Glycogen Phosphorylase b in complex with AZT


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES6.728910mM Bes buffer, 3mM DDT, pH6.7, SMALL TUBES, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4649.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.436α = 90
b = 128.436β = 90
c = 116.31γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC QUANTUM 42007-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X130.8EMBL/DESY, HAMBURGX13

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
12.1430990.03617.26.65362853628-3
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)
12.142.1898.60.4974.76.7

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 SYNTHESISTHROUGHOUT2PRJ2.1424.7350869272399.010.185160.18340.21882RANDOM33.776
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]
0.840.84-1.68
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.367
r_dihedral_angle_4_deg18.623
r_dihedral_angle_3_deg15.42
r_dihedral_angle_1_deg5.148
r_scangle_it2.07
r_scbond_it1.245
r_angle_refined_deg1.044
r_mcangle_it0.972
r_mcbond_it0.555
r_nbtor_refined0.303
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.367
r_dihedral_angle_4_deg18.623
r_dihedral_angle_3_deg15.42
r_dihedral_angle_1_deg5.148
r_scangle_it2.07
r_scbond_it1.245
r_angle_refined_deg1.044
r_mcangle_it0.972
r_mcbond_it0.555
r_nbtor_refined0.303
r_nbd_refined0.182
r_symmetry_vdw_refined0.164
r_symmetry_hbond_refined0.11
r_xyhbond_nbd_refined0.108
r_chiral_restr0.076
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6628
Nucleic Acid Atoms
Solvent Atoms272
Heterogen Atoms19

Software

Software
Software NamePurpose
REFMACrefinement
ADSCdata collection
DENZOdata reduction
SCALEPACKdata scaling