1W77

2C-methyl-D-erythritol 4-phosphate cytidylyltransferase (IspD) from Arabidopsis thaliana


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1I52PDB ENTRY 1I52

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1 M HEPES PH 7.5, 0.05 M CADMIUM SULFATE, 1 M SODIUM ACETATE, 0.04 COPPER(II) CHLORIDE
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.496α = 90
b = 74.496β = 90
c = 223.026γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray160CCDADSC CCDMIRRORS2003-09-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
1229.7599.80.0522.316.916508
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)
122.0799.40.432.8

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 REPLACEMENTTHROUGHOUTPDB ENTRY 1I52227.951567483399.80.2370.2320.349RANDOM50.92
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]
0.050.020.05-0.07
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.588
r_dihedral_angle_3_deg21.323
r_dihedral_angle_4_deg21.091
r_scangle_it18.78
r_scbond_it16.556
r_mcangle_it11.302
r_dihedral_angle_1_deg9.782
r_mcbond_it9.567
r_angle_refined_deg1.652
r_nbtor_refined0.33
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.588
r_dihedral_angle_3_deg21.323
r_dihedral_angle_4_deg21.091
r_scangle_it18.78
r_scbond_it16.556
r_mcangle_it11.302
r_dihedral_angle_1_deg9.782
r_mcbond_it9.567
r_angle_refined_deg1.652
r_nbtor_refined0.33
r_symmetry_vdw_refined0.324
r_xyhbond_nbd_refined0.299
r_nbd_refined0.298
r_symmetry_hbond_refined0.269
r_chiral_restr0.117
r_bond_refined_d0.016
r_gen_planes_refined0.011
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
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 Atoms1640
Nucleic Acid Atoms
Solvent Atoms166
Heterogen Atoms26

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
BEASTphasing