3QHD

Crystal structure of 2-C-METHYL-D-ERYTHRITOL 2,4-CYCLODIPHOSPHATE Synthase from BURKHOLDERIA PSEUDOMALLEI bound to CYTIDINE, FOL795 and FOL955


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3MBMPDB entry 3MBM

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8289BupsA.00122.a.A1 W29971. 27 MG/ML PROTEIN IN 20% PEG 4000, 100 MM TRIS, 200 MM NACL, 5 MM ZNCL2. CRYSTALS SOAKED IN 25 MM LIGANDS IN SAME BUFFER FOR 3 WEEKS, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.0539.98

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.82α = 90
b = 67.95β = 96.3
c = 60.22γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU SATURN 944+2010-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU FR-E+ SUPERBRIGHT1.54178

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
11.72097.70.02330.3650822-325.006
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)
11.71.7480.50.1255.59

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 3MBM1.719.9550777259097.70.15840.15690.1864RANDOM22.0549
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]
0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.802
r_dihedral_angle_4_deg15.904
r_dihedral_angle_3_deg12.438
r_dihedral_angle_1_deg5.242
r_scangle_it2.659
r_scbond_it1.69
r_angle_refined_deg1.398
r_mcangle_it1.005
r_mcbond_it0.592
r_chiral_restr0.089
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.802
r_dihedral_angle_4_deg15.904
r_dihedral_angle_3_deg12.438
r_dihedral_angle_1_deg5.242
r_scangle_it2.659
r_scbond_it1.69
r_angle_refined_deg1.398
r_mcangle_it1.005
r_mcbond_it0.592
r_chiral_restr0.089
r_bond_refined_d0.011
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3457
Nucleic Acid Atoms
Solvent Atoms383
Heterogen Atoms81

Software

Software
Software NamePurpose
XSCALEdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction