1QKI

X-RAY STRUCTURE OF HUMAN GLUCOSE 6-PHOSPHATE DEHYDROGENASE (VARIANT CANTON R459L) COMPLEXED WITH STRUCTURAL NADP+


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1DPGPDB ENTRY 1DPG

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.8HANGING DROP VAPOUR DIFFUSION. 1+1 MICROLITER DROPS IN THE WELL 0.1M SODIUM CITRATE, 0.05M GLYCOLIC ACID, PH 5.8. PROTEIN CONCENTRATION 10MG/ML
Crystal Properties
Matthews coefficientSolvent content
3.0459.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 128.9α = 90
b = 208.7β = 90
c = 214.3γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMIRRORS1997-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSRS BEAMLINE PX9.60.870, 1.488SRSPX9.6

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
132585.30.1115.22.2988644
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
133.274.70.5651.41.8

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 REPLACEMENTFREE R-VALUEPDB ENTRY 1DPG32598864491885.30.2470.2470.294RANDOM IN THIN SHELLS
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_d22.14
x_mcangle_it5.24
x_scangle_it5.24
x_mcbond_it3.45
x_scbond_it3.45
x_angle_deg1.54
x_improper_angle_d1.17
x_bond_d0.008
x_bond_d_na
x_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
x_dihedral_angle_d22.14
x_mcangle_it5.24
x_scangle_it5.24
x_mcbond_it3.45
x_scbond_it3.45
x_angle_deg1.54
x_improper_angle_d1.17
x_bond_d0.008
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms31154
Nucleic Acid Atoms
Solvent Atoms55
Heterogen Atoms454

Software

Software
Software NamePurpose
X-PLORrefinement
DENZOdata reduction
SCALAdata scaling
X-PLORphasing