2J1O

Geranylgeranyl diphosphate synthase from Sinapis alba


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
110pH 10.00
Crystal Properties
Matthews coefficientSolvent content
3.2962.61

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.81α = 90
b = 71.81β = 90
c = 127.85γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SASLSX06SA

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
125099.10.0617.28.526607-3
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)
122.296.50.315.57

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 DIFFRACTIONSIRASTHROUGHOUT24525071132899.80.1960.1950.23RANDOM21.69
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]
-1.13-0.56-1.131.69
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.067
r_dihedral_angle_3_deg16.334
r_dihedral_angle_4_deg11.182
r_dihedral_angle_1_deg5.423
r_scangle_it3.58
r_scbond_it2.639
r_angle_refined_deg1.563
r_mcangle_it1.495
r_mcbond_it1.239
r_angle_other_deg1.054
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.067
r_dihedral_angle_3_deg16.334
r_dihedral_angle_4_deg11.182
r_dihedral_angle_1_deg5.423
r_scangle_it3.58
r_scbond_it2.639
r_angle_refined_deg1.563
r_mcangle_it1.495
r_mcbond_it1.239
r_angle_other_deg1.054
r_mcbond_other0.29
r_symmetry_vdw_other0.279
r_nbd_refined0.236
r_symmetry_vdw_refined0.214
r_nbd_other0.19
r_nbtor_refined0.179
r_symmetry_hbond_refined0.169
r_xyhbond_nbd_refined0.142
r_chiral_restr0.1
r_nbtor_other0.089
r_bond_refined_d0.018
r_gen_planes_refined0.006
r_bond_other_d0.003
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1912
Nucleic Acid Atoms
Solvent Atoms87
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XSCALEdata scaling