2PKQ

Crystal structure of the photosynthetic A2B2-glyceraldehyde-3-phosphate dehydrogenase, complexed with NADP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1RM4PDB ENTRY 1RM4

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.52772.0-2.5 M ammonium sulfate, 0.1 M potassium phosphate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
3.5265.01

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 186.147α = 90
b = 215.687β = 102.52
c = 81.469γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 4mirrors2003-05-03MSINGLE WAVELENGTH
21x-ray100CCDADSC QUANTUM 4mirrors2003-05-03MSINGLE WAVELENGTH
31x-ray100CCDMAR CCD 165 mmmirrors2003-10-18MSINGLE WAVELENGTH
1,2,31
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2
2SYNCHROTRONESRF BEAMLINE ID14-20.933ESRFID14-2
3SYNCHROTRONELETTRA BEAMLINE 5.2R1.000ELETTRA5.2R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
1,2,33.69199.90.3590.3594.513.436736366993-315.9
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1,2,33.63.7399.30.6940.6941.53647

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-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1RM43.690.863673636271180299.90.2610.2610.292RANDOM30.9
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]
6.13-10.387-13.12
RMS Deviations
KeyRefinement Restraint Deviation
c_dihedral_angle_d23.6
c_improper_angle_d5.21
c_scangle_it2.13
c_mcangle_it1.98
c_angle_deg1.9
c_scbond_it1.25
c_mcbond_it1.11
c_bond_d0.014
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms15477
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms363

Software

Software
Software NamePurpose
CNSrefinement
MAR345data collection
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing