3PKO

Crystal structure of geranylgeranyl pyrophosphate synthase from lactobacillus brevis atcc 367 complexed with citrate


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP71.8M AMMONIUM (TRI)CITRATE, PH 7, 10% GLYCEROL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K
Crystal Properties
Matthews coefficientSolvent content
2.3547.7

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.097α = 90
b = 106.705β = 90
c = 132.604γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2010-11-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.985099.90.08885.350182-537.087
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.982.01980.811.44.6

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 DIFFRACTIONSADTHROUGHOUT1.985048395155799.570.184760.183220.23026RANDOM45.513
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]
-1.10.350.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.499
r_dihedral_angle_3_deg16.047
r_dihedral_angle_4_deg14.361
r_scangle_it9.662
r_scbond_it6.967
r_mcangle_it5.811
r_dihedral_angle_1_deg4.814
r_mcbond_it4.247
r_angle_refined_deg1.254
r_chiral_restr0.083
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.499
r_dihedral_angle_3_deg16.047
r_dihedral_angle_4_deg14.361
r_scangle_it9.662
r_scbond_it6.967
r_mcangle_it5.811
r_dihedral_angle_1_deg4.814
r_mcbond_it4.247
r_angle_refined_deg1.254
r_chiral_restr0.083
r_bond_refined_d0.012
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5071
Nucleic Acid Atoms
Solvent Atoms258
Heterogen Atoms19

Software

Software
Software NamePurpose
SHELXmodel building
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing