2Q80

Crystal structure of human geranylgeranyl pyrophosphate synthase bound to GGPP


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherGGPS1 MONOMER BUILT INTO SAD-PHASED MAP (UNPUBLISHED)

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.529325% PEG 3350, 0.2M MG FORMATE, pH 5.50, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.5151.06

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 141.248α = 90
b = 141.248β = 90
c = 211.705γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2005-08-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA1.008SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.747.0899.9127.75951359513
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.721002.836.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTGGPS1 MONOMER BUILT INTO SAD-PHASED MAP (UNPUBLISHED)2.747.085718657186221199.980.204340.204340.202460.25329RANDOM43.886
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]
0.040.04-0.08
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.744
r_dihedral_angle_4_deg18.695
r_dihedral_angle_3_deg17.149
r_dihedral_angle_1_deg5.521
r_scangle_it1.855
r_angle_refined_deg1.389
r_scbond_it1.167
r_angle_other_deg0.947
r_mcangle_it0.735
r_mcbond_it0.438
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.744
r_dihedral_angle_4_deg18.695
r_dihedral_angle_3_deg17.149
r_dihedral_angle_1_deg5.521
r_scangle_it1.855
r_angle_refined_deg1.389
r_scbond_it1.167
r_angle_other_deg0.947
r_mcangle_it0.735
r_mcbond_it0.438
r_symmetry_vdw_other0.286
r_symmetry_vdw_refined0.247
r_nbd_refined0.232
r_nbtor_refined0.191
r_nbd_other0.178
r_xyhbond_nbd_refined0.165
r_symmetry_hbond_refined0.161
r_metal_ion_refined0.103
r_mcbond_other0.094
r_nbtor_other0.089
r_chiral_restr0.07
r_xyhbond_nbd_other0.055
r_bond_refined_d0.014
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms13713
Nucleic Acid Atoms
Solvent Atoms24
Heterogen Atoms176

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
XDSdata reduction
XSCALEdata scaling