4JD0

Structure of the inositol-1-phosphate CTP transferase from T. maritima.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2QQXPDB ENTRY 2QQX

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.52931.8 2.0 M ammonium phosphate and 100 mM LiCl buffered at pH 8.5 with 100 mM Tris, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
3.9168.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 133.09α = 90
b = 133.09β = 90
c = 43.365γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS HTC2009-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-D1.54

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
11.8115.47930.04525.253850038500
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)
11.81.8363.40.412.61287

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 2QQX1.8115.473850036573192593.820.11410.111360.16606RANDOM31.767
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]
0.640.320.64-0.96
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free46.379
r_dihedral_angle_2_deg29.757
r_sphericity_bonded28.252
r_dihedral_angle_3_deg15.36
r_dihedral_angle_4_deg13.972
r_rigid_bond_restr8.052
r_dihedral_angle_1_deg6.493
r_angle_refined_deg2.354
r_chiral_restr0.153
r_bond_refined_d0.024
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free46.379
r_dihedral_angle_2_deg29.757
r_sphericity_bonded28.252
r_dihedral_angle_3_deg15.36
r_dihedral_angle_4_deg13.972
r_rigid_bond_restr8.052
r_dihedral_angle_1_deg6.493
r_angle_refined_deg2.354
r_chiral_restr0.153
r_bond_refined_d0.024
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1939
Nucleic Acid Atoms
Solvent Atoms240
Heterogen Atoms50

Software

Software
Software NamePurpose
CrystalCleardata collection
PHASESphasing
REFMACrefinement
HKL-2000data reduction
SCALEPACKdata scaling