5EX9

Structure of P450 StaF from glycopeptide antibiotic A47934 biosynthesis; glycerol cryo


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3O1A 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP5.22771.2 M NH4PO4, 0.3 M K2HPO4, 0.1 M NH4PO4 citrate (pH 4.2)
Crystal Properties
Matthews coefficientSolvent content
3.4564.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 109.7α = 90
b = 109.7β = 90
c = 93.9γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2010-08-22MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X10SA0.9792SLSX10SA

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym 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
12.25098.40.090.06216.69.633006
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)
12.22.395.50.45.510.3

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 REPLACEMENTTHROUGHOUT3O1A2.247.513185716561000.19220.190760.22011RANDOM36.062
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]
-0.1-0.05-0.10.15
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.049
r_dihedral_angle_4_deg17.626
r_dihedral_angle_3_deg14.427
r_dihedral_angle_1_deg5.083
r_scangle_it2.032
r_scbond_it1.236
r_angle_refined_deg1.071
r_mcangle_it0.747
r_mcbond_it0.381
r_chiral_restr0.072
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg30.049
r_dihedral_angle_4_deg17.626
r_dihedral_angle_3_deg14.427
r_dihedral_angle_1_deg5.083
r_scangle_it2.032
r_scbond_it1.236
r_angle_refined_deg1.071
r_mcangle_it0.747
r_mcbond_it0.381
r_chiral_restr0.072
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_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 Atoms3239
Nucleic Acid Atoms
Solvent Atoms216
Heterogen Atoms91

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Cootmodel building
PHASERphasing
XSCALEdata scaling