2JKC

Crystal Structure of E346D of Tryptophan 7-Halogenase (PrnA)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2AQJPDB ENTRY 2AQJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1100.1M CHES PH10 0.2M NACL 1.6 M (NH4)2SO4
Crystal Properties
Matthews coefficientSolvent content
2.653.5

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.36α = 90
b = 68.36β = 90
c = 276.63γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDRIGAKU CCDOSMIC MIRRORS2008-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU MICROMAX-007 HF

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
12.328.196.60.0914.35297792
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)
12.32.4850.2954.1

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2AQJ2.328.1328173152798.30.1640.1610.21RANDOM18.46
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]
0.50.5-1
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.056
r_dihedral_angle_4_deg20.361
r_dihedral_angle_3_deg13.899
r_dihedral_angle_1_deg6.616
r_scangle_it2.649
r_scbond_it1.674
r_angle_refined_deg1.364
r_mcangle_it1.059
r_mcbond_it0.633
r_nbtor_refined0.302
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.056
r_dihedral_angle_4_deg20.361
r_dihedral_angle_3_deg13.899
r_dihedral_angle_1_deg6.616
r_scangle_it2.649
r_scbond_it1.674
r_angle_refined_deg1.364
r_mcangle_it1.059
r_mcbond_it0.633
r_nbtor_refined0.302
r_symmetry_hbond_refined0.26
r_symmetry_vdw_refined0.198
r_nbd_refined0.192
r_xyhbond_nbd_refined0.151
r_chiral_restr0.09
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4153
Nucleic Acid Atoms
Solvent Atoms396
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
SCALAdata scaling
REFMACphasing