4JXN

CRYSTAL STRUCTURE OF POLYPRENYL SYNTHASE ISP_B (TARGET EFI-509198) FROM Roseobacter denitrificans


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4GP1PDB ENTRY 4GP1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.60.2M CALCIUM CHLORIDE, 0.1M SODIUM ACETATE, PH 4.6, 30% PEG400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K
Crystal Properties
Matthews coefficientSolvent content
2.6453.36

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.49α = 90
b = 115.172β = 90
c = 136.221γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315MIRRORS2013-02-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONNSLS BEAMLINE X29ANSLSX29A

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
12.350980.1117.3917070-5
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.32.341001.58.7

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 4GP12.335.681648853797.80.220.2180.283RANDOM81.29
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]
-3.714.28-0.57
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.521
r_dihedral_angle_3_deg16.055
r_dihedral_angle_4_deg13.772
r_dihedral_angle_1_deg5.225
r_angle_refined_deg1.029
r_angle_other_deg0.734
r_chiral_restr0.053
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.521
r_dihedral_angle_3_deg16.055
r_dihedral_angle_4_deg13.772
r_dihedral_angle_1_deg5.225
r_angle_refined_deg1.029
r_angle_other_deg0.734
r_chiral_restr0.053
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
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_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2235
Nucleic Acid Atoms
Solvent Atoms40
Heterogen Atoms8

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling