4NJO

crystal structure of cofactor(NAD+) bound 3-phosphoglycerate dehydrogenase in Entamoeba histolytica


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.528925% PEG 3350, 100mM Tris pH 7.0-8.0 300mM sodium formate, 5% glycerol , VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
1.9436.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 49.378α = 66.71
b = 56.857β = 66.22
c = 57.259γ = 77.36
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray77IMAGE PLATERIGAKU RAXIS IV++2012-02-15MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-0071.54

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.2252.0995.624702-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.222.390.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 REPLACEMENTTHROUGHOUT2.2252.0923444125795.480.203430.201140.24604RANDOM45.223
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]
-2.64-2.252.034.36-1.84-1.64
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.878
r_dihedral_angle_3_deg14.784
r_dihedral_angle_4_deg12.31
r_dihedral_angle_1_deg5.01
r_mcangle_it1.621
r_mcbond_other1.322
r_scbond_it1.056
r_mcbond_it0.934
r_angle_refined_deg0.918
r_chiral_restr0.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.878
r_dihedral_angle_3_deg14.784
r_dihedral_angle_4_deg12.31
r_dihedral_angle_1_deg5.01
r_mcangle_it1.621
r_mcbond_other1.322
r_scbond_it1.056
r_mcbond_it0.934
r_angle_refined_deg0.918
r_chiral_restr0.064
r_bond_refined_d0.005
r_gen_planes_refined0.002
r_gen_planes_other0.001
r_bond_other_d
r_angle_other_deg
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 Atoms4724
Nucleic Acid Atoms
Solvent Atoms148
Heterogen Atoms64

Software

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