4NAK

Arabidopsis thaliana IspD in complex with pentabromo-pseudilin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4NAIPDB ENTRY 4NAI

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP7.529350 mM HEPES, 50 mM CdSO4, 800 mM KAc, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.448.76

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 75.24α = 90
b = 75.24β = 90
c = 224.14γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2013-02-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06SA1.0SLSX06SA

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
11.83095.80.04219.552214722
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)
11.81.997.30.5363.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (I)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 REPLACEMENTTHROUGHOUTPDB ENTRY 4NAI1.81022214721039110895.770.1940.191940.190590.21821RANDOM45.488
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]
0.420.420.42-1.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.404
r_sphericity_free22.6
r_dihedral_angle_3_deg13.119
r_sphericity_bonded9.371
r_dihedral_angle_4_deg8.245
r_dihedral_angle_1_deg4.849
r_rigid_bond_restr2.443
r_angle_refined_deg1.05
r_chiral_restr0.064
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.404
r_sphericity_free22.6
r_dihedral_angle_3_deg13.119
r_sphericity_bonded9.371
r_dihedral_angle_4_deg8.245
r_dihedral_angle_1_deg4.849
r_rigid_bond_restr2.443
r_angle_refined_deg1.05
r_chiral_restr0.064
r_bond_refined_d0.005
r_gen_planes_refined0.004
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1631
Nucleic Acid Atoms
Solvent Atoms69
Heterogen Atoms36

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing