3GVX

Crystal structure of Glycerate dehydrogenase related protein from Thermoplasma acidophilum


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
12980.2M Pottasium phosphate dibasic, 25% peg 3350, 20% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
3.0359.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 66.512α = 90
b = 77.842β = 90
c = 152.654γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMIRRORS2009-03-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
12.25094.40.09414.88.23852521.3
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)
2.212.2971.80.49113.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONSADTHROUGHOUT2.240.423434134341171984.20.240.240.261RANDOM37.6
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]
-0.42-0.220.64
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25
c_scangle_it3.02
c_mcangle_it2.21
c_scbond_it2.04
c_angle_deg1.9
c_mcbond_it1.36
c_improper_angle_d1.11
c_bond_d0.018
c_bond_d_na
c_bond_d_prot
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d25
c_scangle_it3.02
c_mcangle_it2.21
c_scbond_it2.04
c_angle_deg1.9
c_mcbond_it1.36
c_improper_angle_d1.11
c_bond_d0.018
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4471
Nucleic Acid Atoms
Solvent Atoms203
Heterogen Atoms2

Software

Software
Software NamePurpose
CBASSdata collection
SHELXmodel building
SHARPphasing
ARP/wARPmodel building
CNSrefinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXphasing