3LSN

Crystal structure of putative geranyltranstransferase from PSEUDOMONAS fluorescens PF-5 complexed with magnesium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3LJIPDB entry 3LJI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.52980.2 M Mg chloride, 0.1 M HEPES, 25% PEG 3350, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties
Matthews coefficientSolvent content
238.45

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.182α = 90
b = 47.875β = 120.78
c = 75.982γ = 90
Symmetry
Space GroupC 1 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 3152010-01-28SINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29A0.9791NSLSX29A

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
11.3550750.06114.13.342940
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)
11.351.3710.40.3991.6294

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 3LJI1.352042920218375.10.180.1790.201RANDOM19.314
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]
-0.210.570.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.079
r_dihedral_angle_4_deg18.032
r_dihedral_angle_3_deg14.816
r_scbond_it6.651
r_dihedral_angle_1_deg4.008
r_mcangle_it2.946
r_scangle_it1.334
r_angle_refined_deg1.205
r_mcbond_it0.925
r_chiral_restr0.074
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.079
r_dihedral_angle_4_deg18.032
r_dihedral_angle_3_deg14.816
r_scbond_it6.651
r_dihedral_angle_1_deg4.008
r_mcangle_it2.946
r_scangle_it1.334
r_angle_refined_deg1.205
r_mcbond_it0.925
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.006
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2081
Nucleic Acid Atoms
Solvent Atoms256
Heterogen Atoms3

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
CBASSdata collection
HKL-2000data reduction