2J1P

Geranylgeranyl diphosphate synthase from Sinapis alba in complex with GGPP


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.2344.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 53.803α = 90
b = 91.551β = 96.89
c = 56.286γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARRESEARCHMMAD
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
11.83495.60.0410.6294523-3
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)
11.81.991.50.481.6

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 DIFFRACTIONMADTHROUGHOUT1.83246010245896.70.1720.170.209RANDOM17.74
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]
-0.19-0.040.54-0.36
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.66
r_dihedral_angle_4_deg16.436
r_dihedral_angle_3_deg14.485
r_dihedral_angle_1_deg5.297
r_scangle_it3.884
r_scbond_it2.798
r_angle_refined_deg1.689
r_mcangle_it1.462
r_mcbond_it1.29
r_angle_other_deg1.064
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.66
r_dihedral_angle_4_deg16.436
r_dihedral_angle_3_deg14.485
r_dihedral_angle_1_deg5.297
r_scangle_it3.884
r_scbond_it2.798
r_angle_refined_deg1.689
r_mcangle_it1.462
r_mcbond_it1.29
r_angle_other_deg1.064
r_symmetry_vdw_other0.284
r_symmetry_vdw_refined0.236
r_nbd_refined0.228
r_nbd_other0.195
r_nbtor_refined0.178
r_xyhbond_nbd_refined0.151
r_symmetry_hbond_refined0.134
r_chiral_restr0.103
r_nbtor_other0.089
r_bond_refined_d0.019
r_gen_planes_refined0.006
r_bond_other_d0.002
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_mcbond_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 Atoms4173
Nucleic Acid Atoms
Solvent Atoms190
Heterogen Atoms47

Software

Software
Software NamePurpose
REFMACrefinement