4NAL

Arabidopsis thaliana IspD in complex with tribromodichloro-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
2.447.77

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 74.46α = 90
b = 74.46β = 90
c = 224.5γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELPSI PILATUS 6M2012-12-01MSINGLE 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
11.83099.90.04227.29.62269222
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)
11.81.999.60.6254

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 REPLACEMENTTHROUGHOUTPDB ENTRY 4NAI1.8102269221557113599.930.210.207860.205320.24582RANDOM46.809
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]
0.230.230.23-0.74
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.756
r_sphericity_free23.104
r_dihedral_angle_3_deg13.955
r_sphericity_bonded9.819
r_dihedral_angle_4_deg8.072
r_dihedral_angle_1_deg4.826
r_rigid_bond_restr2.126
r_angle_refined_deg1.062
r_chiral_restr0.067
r_bond_refined_d0.005
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.756
r_sphericity_free23.104
r_dihedral_angle_3_deg13.955
r_sphericity_bonded9.819
r_dihedral_angle_4_deg8.072
r_dihedral_angle_1_deg4.826
r_rigid_bond_restr2.126
r_angle_refined_deg1.062
r_chiral_restr0.067
r_bond_refined_d0.005
r_gen_planes_refined0.005
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1661
Nucleic Acid Atoms
Solvent Atoms59
Heterogen Atoms37

Software

Software
Software NamePurpose
XDSdata scaling
REFMACrefinement
XDSdata reduction
XSCALEdata scaling
REFMACphasing