1DSS | pdb_00001dss

STRUCTURE OF ACTIVE-SITE CARBOXYMETHYLATED D-GLYCERALDEHYDE-3-PHOSPHATE DEHYDROGENASE FROM PALINURUS VERSICOLOR


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherHOLO-GAPDH FROM PALINURUS VERSICOLOR (2.0A)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.1290THE PROTEIN SOLUTIONS CONTAINED 0.5MM NAD+, 1.0MM EDTA, 1.6M AMMONIUM SULFATE IN 0.1M PHOSPHATE BUFFER(PH 6.1) AND AN ENZYME CONCENTRATION OF 8MG/ML; THE SOLUTION IN RESERVOIR CONTAINED 2.7M AMMONIUM SULFATE IN SAME BUFFER, ROOM TEMPERATURE OF 17 DEGREES C., temperature 290K
Crystal Properties
Matthews coefficientSolvent content
3.2762

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.1α = 90
b = 99.61β = 114.4
c = 80.69γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray280DIFFRACTOMETERWEISSENBERG1990-11-30M
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-6APhoton FactoryBL-6A

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
11.8150940.0794.21.077803014.73
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)
11.81.8856.50.0792.11.07

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTHOLO-GAPDH FROM PALINURUS VERSICOLOR (2.0A)1.886358730596180.960.17170.17170.160.218RANDOM17.25
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]
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d25.92
x_angle_deg2.65
x_improper_angle_d1.79
x_bond_d0.012
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d25.92
x_angle_deg2.65
x_improper_angle_d1.79
x_bond_d0.012
x_bond_d_na
x_bond_d_prot
x_angle_d
x_angle_d_na
x_angle_d_prot
x_angle_deg_na
x_angle_deg_prot
x_dihedral_angle_d_na
x_dihedral_angle_d_prot
x_improper_angle_d_na
x_improper_angle_d_prot
x_mcbond_it
x_mcangle_it
x_scbond_it
x_scangle_it
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5020
Nucleic Acid Atoms
Solvent Atoms400
Heterogen Atoms108

Software

Software
Software NamePurpose
X-PLORmodel building
X-PLORrefinement
WEISdata reduction
WEISdata scaling
X-PLORphasing