2ZRU

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


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
2.6453.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 100.745α = 90
b = 100.745β = 90
c = 336.829γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray95CCDADSC QUANTUM 210mirror2008-02-20MMAD
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000, 1.13980, 1.14022, 1.04000Photon FactoryAR-NW12A

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
11.995099.40.08724.68.411940125
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)
11.992.0696.90.2688.38.1

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 DIFFRACTIONMADTHROUGHOUT237.5110468582697.990.187470.18560.22253RANDOM29.544
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.612
r_dihedral_angle_4_deg24.544
r_dihedral_angle_3_deg17.17
r_dihedral_angle_1_deg5.76
r_scangle_it3.216
r_scbond_it2.108
r_angle_refined_deg1.462
r_mcangle_it1.324
r_mcbond_it0.854
r_nbtor_refined0.311
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.612
r_dihedral_angle_4_deg24.544
r_dihedral_angle_3_deg17.17
r_dihedral_angle_1_deg5.76
r_scangle_it3.216
r_scbond_it2.108
r_angle_refined_deg1.462
r_mcangle_it1.324
r_mcbond_it0.854
r_nbtor_refined0.311
r_symmetry_vdw_refined0.217
r_nbd_refined0.214
r_xyhbond_nbd_refined0.169
r_symmetry_hbond_refined0.149
r_chiral_restr0.105
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10996
Nucleic Acid Atoms
Solvent Atoms728
Heterogen Atoms124

Software

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