1VGT

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


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.1442.64

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 40.866α = 90
b = 78.783β = 90
c = 138.385γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-rayCCDMARRESEARCHMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 32-ID0.9795, 0.9795, 0.9641, 1.5418APS32-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
11.822.6596.80.05817.96.64089940899
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)
11.81.996.80.4554.66.1

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 DIFFRACTIONSe-Met MAD phasing1.822.654089820710.2240.25330.219
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]
0.9310.386-1.316
RMS Deviations
KeyRefinement Restraint Deviation
p_scangle_it4.985
p_scbond_it3.402
p_mcangle_it3.318
p_planar_tor2.878
p_angle_d2.398
p_mcbond_it2.151
p_chiral_restr0.174
p_bond_d0.028
p_plane_restr0.013
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3176
Nucleic Acid Atoms
Solvent Atoms197
Heterogen Atoms

Software

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