2ZRZ

Crystal structure of Sulfolobus shibatae isopentenyl diphosphate isomerase in complex with reduced FMN and DMAPP


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION829330% PEG 400, 0.2M sodium citrate, 0.1M Tris-HCl, pH 8.0, VAPOR DIFFUSION, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.6353.25

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.879α = 90
b = 100.879β = 90
c = 334.864γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 270mirror2008-06-29MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE BL-17A1.0000, 1.13980, 1.14022, 1.04000Photon FactoryBL-17A

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
12.95099.60.0922.111.93943063.6
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)
12.9396.90.4122.56.1

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 DIFFRACTIONMADTHROUGHOUT2.948.8537374197099.490.193180.192120.2129RANDOM45.543
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]
-0.01-0.010.02
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.368
r_dihedral_angle_4_deg23.408
r_dihedral_angle_3_deg19.83
r_dihedral_angle_1_deg5.53
r_scangle_it2.561
r_angle_refined_deg1.572
r_scbond_it1.449
r_mcangle_it1.265
r_mcbond_it0.734
r_symmetry_vdw_refined0.344
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.368
r_dihedral_angle_4_deg23.408
r_dihedral_angle_3_deg19.83
r_dihedral_angle_1_deg5.53
r_scangle_it2.561
r_angle_refined_deg1.572
r_scbond_it1.449
r_mcangle_it1.265
r_mcbond_it0.734
r_symmetry_vdw_refined0.344
r_nbtor_refined0.311
r_symmetry_hbond_refined0.259
r_nbd_refined0.212
r_chiral_restr0.177
r_xyhbond_nbd_refined0.151
r_bond_refined_d0.012
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms11232
Nucleic Acid Atoms
Solvent Atoms172
Heterogen Atoms184

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SHARPphasing