3E3L

The R-state Glycogen Phosphorylase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 9GPBpdb entry 9gpb

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1SMALL TUBES7.52891.1-1.3 M ammonium sulfate, 10mM beta-glycerophosphate buffer pH 7.5, 0.5mM EDTA, SMALL TUBES, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.4148.93

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 118.895α = 90
b = 189.92β = 109.27
c = 88.16γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray293CCDMARMOSAIC 225 mm CCD2008-02-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.10.97976SRSPX10.1

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
12.593099.60.06411.73.4112937107281-3
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)
12.62.6499.60.3583.893.3

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 (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONFOURIER SYNTHESISTHROUGHOUTpdb entry 9gpb2.5929.59107281107281565499.290.209580.206560.210.265770.27RANDOM49.826
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]
-1.95-0.361.71
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.841
r_dihedral_angle_3_deg21.501
r_dihedral_angle_4_deg19.187
r_dihedral_angle_1_deg6.261
r_scangle_it1.889
r_angle_refined_deg1.341
r_scbond_it1.125
r_mcangle_it0.851
r_mcbond_it0.471
r_nbtor_refined0.312
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms26363
Nucleic Acid Atoms
Solvent Atoms110
Heterogen Atoms60

Software

Software
Software NamePurpose
REFMACrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing