4NFY

Crystal Structure of 3-phosphoglycerate Dehydrogenase from Entamoeba histolytica


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.528920% PEG, 100mM Tris-cl, 350mM sodium formate, 5% Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.2545.41

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.906α = 90
b = 85.906β = 90
c = 84.492γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77.15CCDMAR CCD 165 mm2011-09-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM140.97ESRFBM14

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.4585.910.04736.44.222458
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)
12.452.490.2027.43.9

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 REPLACEMENTTHROUGHOUT1WWK2.4585.9121307115098.970.197280.194030.25895RANDOM48.265
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]
2.582.58-5.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.067
r_dihedral_angle_4_deg19.379
r_dihedral_angle_3_deg14.816
r_dihedral_angle_1_deg5.849
r_mcangle_it3.35
r_scbond_it2.381
r_mcbond_it2.075
r_mcbond_other2.074
r_angle_refined_deg1.176
r_angle_other_deg0.712
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.067
r_dihedral_angle_4_deg19.379
r_dihedral_angle_3_deg14.816
r_dihedral_angle_1_deg5.849
r_mcangle_it3.35
r_scbond_it2.381
r_mcbond_it2.075
r_mcbond_other2.074
r_angle_refined_deg1.176
r_angle_other_deg0.712
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.003
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4730
Nucleic Acid Atoms
Solvent Atoms135
Heterogen Atoms16

Software

Software
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling