X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1P5GPMM/PGM bound to glucose 6-phosphate

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.5Na K tartrate, Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 100K
Crystal Properties
Matthews coefficientSolvent content
2.244.22

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 70.7α = 90
b = 74.193β = 90
c = 84.836γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2003-02-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 14-BM-C0.9APS14-BM-C

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
11.62599.10.07432.18.2591655863318.6
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)
11.61.6698.30.4913.8

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 DIFFRACTIONrigid body refinement followed by regular refinementTHROUGHOUTPMM/PGM bound to glucose 6-phosphate1.6255951456042294599.150.16210.15680.155650.17901RANDOM14.863
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]
-0.52-0.420.94
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.878
r_scangle_it3.442
r_scbond_it2.078
r_angle_refined_deg1.387
r_mcangle_it1.268
r_angle_other_deg0.998
r_mcbond_it0.692
r_symmetry_vdw_other0.278
r_symmetry_vdw_refined0.246
r_nbd_other0.244
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg5.878
r_scangle_it3.442
r_scbond_it2.078
r_angle_refined_deg1.387
r_mcangle_it1.268
r_angle_other_deg0.998
r_mcbond_it0.692
r_symmetry_vdw_other0.278
r_symmetry_vdw_refined0.246
r_nbd_other0.244
r_nbd_refined0.214
r_xyhbond_nbd_refined0.162
r_symmetry_hbond_refined0.14
r_metal_ion_refined0.09
r_chiral_restr0.085
r_nbtor_other0.082
r_bond_refined_d0.011
r_gen_planes_refined0.006
r_gen_planes_other0.005
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3436
Nucleic Acid Atoms
Solvent Atoms464
Heterogen Atoms17

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling
CNSphasing