5LHK

Bottromycin maturation enzyme BotP in complex with Mn


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP291PEG 4000 (10 % w/v)), MES pH 6.5 (0.1 M)
Crystal Properties
Matthews coefficientSolvent content
3.2462.07

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 151.51α = 90
b = 151.51β = 90
c = 101.19γ = 120
Symmetry
Space GroupP 63 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 2M-F2015-09-07MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSLS BEAMLINE X06DA1.89SLSX06DA

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
12.3247.211000.14226.837.830149
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)
12.322.3899.90.7365.935.7

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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 DIFFRACTIONSADTHROUGHOUT2.3247.2128658146699.940.148910.146780.18977RANDOM30.514
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]
-0.85-0.42-0.852.75
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free26.072
r_dihedral_angle_2_deg24.986
r_dihedral_angle_4_deg17.79
r_dihedral_angle_3_deg13.088
r_sphericity_bonded8.22
r_dihedral_angle_1_deg5.963
r_long_range_B_refined3.951
r_long_range_B_other3.417
r_scangle_other2.661
r_scbond_it2.363
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free26.072
r_dihedral_angle_2_deg24.986
r_dihedral_angle_4_deg17.79
r_dihedral_angle_3_deg13.088
r_sphericity_bonded8.22
r_dihedral_angle_1_deg5.963
r_long_range_B_refined3.951
r_long_range_B_other3.417
r_scangle_other2.661
r_scbond_it2.363
r_scbond_other2.358
r_mcangle_it2.304
r_mcangle_other2.304
r_mcbond_it1.836
r_mcbond_other1.836
r_rigid_bond_restr1.532
r_angle_refined_deg1.26
r_angle_other_deg0.92
r_chiral_restr0.064
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.002
r_gen_planes_other0.001
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3304
Nucleic Acid Atoms
Solvent Atoms330
Heterogen Atoms6

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
PHENIXphasing