2PNY

Structure of Human Isopentenyl-diphosphate Delta-isomerase 2


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2ICJPDB entry 2ICJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7291Protein buffer: 10 mg/mL Protein, 0.1 M NaCl, 0.05 M Tris-HCl pH 8.0, 0.001 M TCEP, 0.001 M CaCl2, 0.001 M MgCl2, 0.001 M MnCl2. Precipitant: 2 M Na/K PO4, pH 7.0. Cryoprotectant: 20% Glycerol, VAPOR DIFFUSION, SITTING DROP, temperature 291.0K
Crystal Properties
Matthews coefficientSolvent content
2.2545.24

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.897α = 90
b = 52.815β = 90
c = 96.391γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV++2007-04-19MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU1.54178

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.82598.70.05636.9572444724447-3
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.8686.80.2389.66.72101

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 2ICJ1.8124.162439423192120299.930.149310.147590.18203RANDOM13.151
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]
1.29-0.57-0.72
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.426
r_dihedral_angle_4_deg21.882
r_dihedral_angle_3_deg12.608
r_dihedral_angle_1_deg6.317
r_scangle_it3.597
r_scbond_it2.517
r_angle_refined_deg1.618
r_mcangle_it1.318
r_mcbond_it0.968
r_nbtor_refined0.309
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg28.426
r_dihedral_angle_4_deg21.882
r_dihedral_angle_3_deg12.608
r_dihedral_angle_1_deg6.317
r_scangle_it3.597
r_scbond_it2.517
r_angle_refined_deg1.618
r_mcangle_it1.318
r_mcbond_it0.968
r_nbtor_refined0.309
r_nbd_refined0.212
r_metal_ion_refined0.184
r_symmetry_vdw_refined0.162
r_symmetry_hbond_refined0.135
r_xyhbond_nbd_refined0.131
r_chiral_restr0.123
r_bond_refined_d0.019
r_gen_planes_refined0.008
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1931
Nucleic Acid Atoms
Solvent Atoms187
Heterogen Atoms29

Software

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