5YO8

Crystal structure of beta-C25/C30/C35-prene synthase


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION929315% PEG 3350, 0.1M BICINE-Na (pH 9.0), 0.2M Ammonium phosphate dibasic
Crystal Properties
Matthews coefficientSolvent content
2.4449.66

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.35α = 90
b = 151.67β = 110.03
c = 53.84γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2MMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NE3A1.000Photon FactoryAR-NE3A

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
11.645094.40.05811.33.2492698
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)
11.641.6887.70.67823.22

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 DIFFRACTIONSADTHROUGHOUT1.645088062459294.540.205470.204210.22934RANDOM29.429
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]
0.780.850.08-1.17
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.442
r_dihedral_angle_4_deg16.527
r_dihedral_angle_3_deg12.258
r_dihedral_angle_1_deg4.97
r_long_range_B_refined4.467
r_long_range_B_other4.252
r_angle_refined_deg1.119
r_mcangle_it0.984
r_mcangle_other0.983
r_scangle_other0.971
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.442
r_dihedral_angle_4_deg16.527
r_dihedral_angle_3_deg12.258
r_dihedral_angle_1_deg4.97
r_long_range_B_refined4.467
r_long_range_B_other4.252
r_angle_refined_deg1.119
r_mcangle_it0.984
r_mcangle_other0.983
r_scangle_other0.971
r_angle_other_deg0.893
r_scbond_it0.566
r_scbond_other0.566
r_mcbond_it0.554
r_mcbond_other0.554
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.005
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms5762
Nucleic Acid Atoms
Solvent Atoms549
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction