1J0X

Crystal structure of the rabbit muscle glyceraldehyde-3-phosphate dehydrogenase (GAPDH)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GD1Dimer of PDB ENTRY 1GD1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8293PEG 3350, HEPES, K3-citrate, microseeding, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.4850.04

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 81.7α = 90
b = 98.5β = 90
c = 183.1γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMirrorMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM1A0.8ESRFBM1A

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
12.417.9396.60.034584245652127.1
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
2.42.4986.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTDimer of PDB ENTRY 1GD12.417.935842456188285396.20.2030.239RANDOM31.1
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]
-9.170.159.02
RMS Deviations
KeyRefinement Restraint Deviation
c_angle_deg1.44
c_bond_d0.01
c_dihedral_angle_d
c_improper_angle_d
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10044
Nucleic Acid Atoms
Solvent Atoms473
Heterogen Atoms88

Software

Software
Software NamePurpose
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
TRUNCATEdata reduction
AMoREphasing
CNSrefinement
CCP4data scaling