5KCG | pdb_00005kcg

Crystal structure of the aromatic prenyltransferase AtaPT (apo state) from Aspergillus terreus A8-4


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3I4Z 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP62890.1 M Bis-Tris pH 6.0, 0.2 M (NH4)2SO4, 17% PEG 3350, 3.3% DDM
Crystal Properties
Matthews coefficientSolvent content
2.4649.99

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 96.2α = 90
b = 135.81β = 90
c = 69.52γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2013-06-20MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRF BEAMLINE BL17U0.97SSRFBL17U

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)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
11.9135.8199.10.0880.0980.04311.14.97170771707
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)
11.921000.4161.75

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3I4Z1.948.5868155349198.830.193840.191710.20.235760.24RANDOM30.338
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]
-1.760.960.8
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.758
r_dihedral_angle_3_deg15.08
r_dihedral_angle_4_deg12.413
r_long_range_B_refined7.28
r_long_range_B_other7.259
r_dihedral_angle_1_deg6.482
r_scangle_other5.808
r_scbond_it3.958
r_scbond_other3.957
r_mcangle_other3.855
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.758
r_dihedral_angle_3_deg15.08
r_dihedral_angle_4_deg12.413
r_long_range_B_refined7.28
r_long_range_B_other7.259
r_dihedral_angle_1_deg6.482
r_scangle_other5.808
r_scbond_it3.958
r_scbond_other3.957
r_mcangle_other3.855
r_mcangle_it3.854
r_mcbond_it2.866
r_mcbond_other2.863
r_angle_refined_deg1.828
r_angle_other_deg1.251
r_chiral_restr0.119
r_bond_refined_d0.019
r_gen_planes_refined0.011
r_bond_other_d0.006
r_gen_planes_other0.005
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6301
Nucleic Acid Atoms
Solvent Atoms252
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing
Cootmodel building
SCALAdata scaling
MOSFLMdata processing