2YYY

Crystal structure of Glyceraldehyde-3-phosphate dehydrogenase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1CF2 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1oil-batch8.52930.2M magnesium chloride hexahydrate, 0.08M tris hydrochloride, pH 8.5, 24%(w/v) PEG4000, 20%(v/v) glycerol anhydrous, oil-batch, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4650.03

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.398α = 90
b = 152.04β = 90
c = 118.552γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDMARMOSAIC 225 mm CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX10.11.117SRSPX10.1

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
11.855097.10.0664.56438962507-3
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)
1.851.9278.10.2382.94944

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 REPLACEMENTTHROUGHOUT1CF21.852059323314697.10.170690.169230.19795RANDOM18.797
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]
0.860.04-0.89
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.116
r_scangle_it3.886
r_scbond_it2.418
r_angle_refined_deg1.507
r_mcangle_it1.296
r_mcbond_it0.724
r_symmetry_hbond_refined0.221
r_nbd_refined0.21
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.132
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_1_deg6.116
r_scangle_it3.886
r_scbond_it2.418
r_angle_refined_deg1.507
r_mcangle_it1.296
r_mcbond_it0.724
r_symmetry_hbond_refined0.221
r_nbd_refined0.21
r_symmetry_vdw_refined0.174
r_xyhbond_nbd_refined0.132
r_chiral_restr0.099
r_bond_refined_d0.016
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5328
Nucleic Acid Atoms
Solvent Atoms348
Heterogen Atoms96

Software

Software
Software NamePurpose
REFMACrefinement
MAR345dtbdata collection
HKL-2000data reduction
SCALEPACKdata scaling
MOLREPphasing