3F0E

Crystal structure of 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase from Burkholderia pseudomallei


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.9289JCSG+ screen condition a5, 20% PEG 3350, 0.2 M magnesium formate, 34.4 mg/mL protein, 0.4/0.4 uL drops, crystal ID 200155a5, pH 5.9, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0740.49

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 116.765α = 90
b = 68.456β = 96.71
c = 60.882γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 9442008-08-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF1.54178

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
12.0560.4195.80.07518.33.728805
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)
12.052.1279.60.2214.42.92396

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 DIFFRACTIONpdb entry 3F0DTHROUGHOUT2.055028796145695.560.2070.2050.246RANDOM22.365
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]
-1.110.042.04-0.91
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.593
r_dihedral_angle_4_deg16.42
r_dihedral_angle_3_deg14.164
r_dihedral_angle_1_deg4.758
r_scangle_it1.759
r_scbond_it1.041
r_angle_refined_deg0.984
r_mcangle_it0.754
r_mcbond_it0.406
r_chiral_restr0.065
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.593
r_dihedral_angle_4_deg16.42
r_dihedral_angle_3_deg14.164
r_dihedral_angle_1_deg4.758
r_scangle_it1.759
r_scbond_it1.041
r_angle_refined_deg0.984
r_mcangle_it0.754
r_mcbond_it0.406
r_chiral_restr0.065
r_bond_refined_d0.007
r_gen_planes_refined0.003
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3351
Nucleic Acid Atoms
Solvent Atoms249
Heterogen Atoms4

Software

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