3H4I

Chimeric Glycosyltransferase for the generation of novel natural products


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1PN3PDB ENTRY 1PN3

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.53000.1M Tris-HCL, 1.2-2M ammonium sulphate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.957.55

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 111.48α = 90
b = 129.83β = 90
c = 67.44γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMAR CCD 130 mm2007-12-05MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM160.98ESRFBM16

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
11.329.9299.90.074711925922
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)
1.31.371000.569717244

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Cut-off Sigma (F)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 1PN31.329.252143104113256597599.920.170.164810.163820.18383RANDOM14.492
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.455
r_dihedral_angle_4_deg17.021
r_dihedral_angle_3_deg10.105
r_dihedral_angle_1_deg5.149
r_scbond_it2.653
r_scangle_it2.59
r_rigid_bond_restr2.532
r_sphericity_free2.097
r_sphericity_bonded1.898
r_angle_refined_deg1.222
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.455
r_dihedral_angle_4_deg17.021
r_dihedral_angle_3_deg10.105
r_dihedral_angle_1_deg5.149
r_scbond_it2.653
r_scangle_it2.59
r_rigid_bond_restr2.532
r_sphericity_free2.097
r_sphericity_bonded1.898
r_angle_refined_deg1.222
r_mcangle_it1.083
r_mcbond_it0.684
r_nbtor_refined0.305
r_nbd_refined0.19
r_symmetry_vdw_refined0.141
r_symmetry_hbond_refined0.128
r_xyhbond_nbd_refined0.106
r_chiral_restr0.073
r_bond_refined_d0.006
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2862
Nucleic Acid Atoms
Solvent Atoms630
Heterogen Atoms46

Software

Software
Software NamePurpose
HKL-2000data collection
AMoREphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling