3ZCS

Rabbit muscle glycogen phosphorylase b in complex with N-(1-naphthoyl) -N-beta-D-glucopyranosyl urea determined at 2.07 A resolution


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QNBPDB ENTRY 2QNB

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.8pH 6.8
Crystal Properties
Matthews coefficientSolvent content
2.550.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.283α = 90
b = 128.283β = 90
c = 116.513γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray298CCDADSC CCD2002-07-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE BW7BEMBL/DESY, HAMBURGBW7B

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
12.0330980.0615.1461970
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)
12.032.0698.20.276.74.1

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2QNB2.0329.558787313898.040.192970.191720.2167RANDOM31.234
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.836
r_dihedral_angle_4_deg19.008
r_dihedral_angle_3_deg13.928
r_dihedral_angle_1_deg5.095
r_scangle_it2.201
r_scbond_it1.256
r_angle_refined_deg0.999
r_mcangle_it0.938
r_mcbond_it0.482
r_chiral_restr0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.836
r_dihedral_angle_4_deg19.008
r_dihedral_angle_3_deg13.928
r_dihedral_angle_1_deg5.095
r_scangle_it2.201
r_scbond_it1.256
r_angle_refined_deg0.999
r_mcangle_it0.938
r_mcbond_it0.482
r_chiral_restr0.07
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6558
Nucleic Acid Atoms
Solvent Atoms275
Heterogen Atoms65

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing