3PQA

Crystal structure of glyceraldehyde-3-phosphate dehydrogenase GapN from Methanocaldococcus jannaschii DSM 2661


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1EUH 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP629835% MPD, 0.1 M MES, 0.2 M lithium sulfate, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
2.1743.35

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 164.574α = 90
b = 77.568β = 116.29
c = 164.279γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-11-16SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9791NSLSX29A

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
11.55078.90.0777.92.7460550
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
1.51.53321.89379

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 REPLACEMENTTHROUGHOUT1EUH1.519.962465631250083.350.18860.18680.2219RANDOM18.3751
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]
0.110.1-0.050.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.834
r_dihedral_angle_3_deg14.169
r_dihedral_angle_4_deg14.132
r_dihedral_angle_1_deg5.919
r_mcangle_it2.616
r_scbond_it2.182
r_mcbond_it1.694
r_angle_refined_deg1.227
r_rigid_bond_restr0.53
r_scangle_it0.503
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.834
r_dihedral_angle_3_deg14.169
r_dihedral_angle_4_deg14.132
r_dihedral_angle_1_deg5.919
r_mcangle_it2.616
r_scbond_it2.182
r_mcbond_it1.694
r_angle_refined_deg1.227
r_rigid_bond_restr0.53
r_scangle_it0.503
r_chiral_restr0.083
r_bond_refined_d0.01
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms14137
Nucleic Acid Atoms
Solvent Atoms1355
Heterogen Atoms35

Software

Software
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction