1VGU

Crystal structure of 4-diphosphocytidyl-2C-methyl-D-erythritol synthase


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
238.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.589α = 90
b = 66.02β = 90
c = 119.475γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARRESEARCHSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-ID0.9795APS32-ID

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
12.839.4792.60.08116.45.599579957
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)
2.82.9592.60.2047.24.9

Refinement

Statistics
Diffraction IDStructure Solution MethodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENT2.839.4799564740.2680.33333.465
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]
-0.954-1.1122.065
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it3.193
p_mcangle_it2.772
p_scbond_it2.012
p_mcbond_it1.675
p_angle_d1.657
p_planar_tor1.36
p_chiral_restr0.105
p_bond_d0.008
p_plane_restr0.007
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3108
Nucleic Acid Atoms
Solvent Atoms34
Heterogen Atoms

Software

Software
Software NamePurpose
MOSFLMdata reduction
SCALAdata scaling
TRUNCATEdata reduction
REFMACrefinement
CCP4data scaling
TRUNCATEdata scaling