5TSO

CRYSTAL STRUCTURE OF GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PIG MUSCLE COMPLEXED WITH ORTHOPHENANTHROLINE AT 1.90 ANGSTROM RESOLUTION


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GD1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP82730.005M 1,10-ORTHOPHENANTHROLINE, 0.05M HEPES, PH 8.0, 54.7%(W/V)AMMONIUM SULFATE,0.005 M EDTA, HANGING DROP, TEMPERATURE 277 K
Crystal Properties
Matthews coefficientSolvent content
3.0359.38

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 86.48α = 90
b = 133.52β = 90
c = 210.32γ = 90
Symmetry
Space GroupI 2 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120PIXELDECTRIS PILATUS3 2M2005-04-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 17-ID1.00APS17-ID

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
11.943.5493.60.066124.387846
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)
11.91.9593.60.1592.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1GD11.943.5487846131993.60.1330.1320.2RANDOM35.4
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]
-0.110.17-0.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.357
r_sphericity_free21.834
r_dihedral_angle_4_deg18.416
r_dihedral_angle_3_deg14.811
r_sphericity_bonded9.266
r_rigid_bond_restr7.026
r_dihedral_angle_1_deg7.016
r_long_range_B_refined5.282
r_long_range_B_other5.123
r_scangle_other5.043
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.357
r_sphericity_free21.834
r_dihedral_angle_4_deg18.416
r_dihedral_angle_3_deg14.811
r_sphericity_bonded9.266
r_rigid_bond_restr7.026
r_dihedral_angle_1_deg7.016
r_long_range_B_refined5.282
r_long_range_B_other5.123
r_scangle_other5.043
r_scbond_it4.634
r_scbond_other4.634
r_mcangle_it4.242
r_mcangle_other4.241
r_mcbond_it3.98
r_mcbond_other3.979
r_angle_refined_deg2.019
r_angle_other_deg0.959
r_chiral_restr0.135
r_bond_refined_d0.019
r_gen_planes_refined0.009
r_bond_other_d0.002
r_gen_planes_other0.001
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_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms7530
Nucleic Acid Atoms
Solvent Atoms883
Heterogen Atoms285

Software

Software
Software NamePurpose
REFMACrefinement
SCALEPACKdata scaling
AMoREphasing
DENZOdata reduction