5NOA

Polysaccharide Lyase BACCELL_00875


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP293.15200 mM sodium malonate 20% polyethylene glycol (PEG) 3350.
Crystal Properties
Matthew coefficientSolvent content
1.8633.81

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 88.398α = 90
b = 88.398β = 90
c = 215.857γ = 120
Symmetry
Space GroupH 3 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2014-04-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9798DiamondI04

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
11.2621.1399.50.998138.887238
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.261.2894.30.5243.9

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 REPLACEMENTTHROUGHOUT4CE71.2621.1381513422997.740.122680.121350.14801RANDOM12.271
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]
0.090.050.09-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.737
r_dihedral_angle_4_deg18.841
r_sphericity_free18.443
r_dihedral_angle_3_deg11.535
r_sphericity_bonded6.215
r_dihedral_angle_1_deg5.743
r_long_range_B_refined2.454
r_long_range_B_other2.349
r_scangle_other2.238
r_rigid_bond_restr1.954
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.737
r_dihedral_angle_4_deg18.841
r_sphericity_free18.443
r_dihedral_angle_3_deg11.535
r_sphericity_bonded6.215
r_dihedral_angle_1_deg5.743
r_long_range_B_refined2.454
r_long_range_B_other2.349
r_scangle_other2.238
r_rigid_bond_restr1.954
r_scbond_it1.864
r_scbond_other1.863
r_mcangle_other1.539
r_mcangle_it1.535
r_angle_refined_deg1.517
r_mcbond_it1.166
r_mcbond_other1.149
r_angle_other_deg0.994
r_chiral_restr0.113
r_bond_refined_d0.013
r_gen_planes_refined0.01
r_bond_other_d0.002
r_gen_planes_other0.002
r_xyhbond_nbd_refined
r_symmetry_metal_ion_other
r_symmetry_vdw_other
r_metal_ion_other
r_metal_ion_refined
r_xyhbond_nbd_other
r_symmetry_hbond_refined
r_nbtor_other
r_scangle_it
r_nbtor_refined
r_nbd_other
r_nbd_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_vdw_refined
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2893
Nucleic Acid Atoms
Solvent Atoms299
Heterogen Atoms

Software

Software
Software NamePurpose
iMOSFLMdata reduction
Aimlessdata scaling
MrBUMPphasing
PHASERphasing
BUCCANEERmodel building
ARPmodel building
WARPmodel building
REFMACrefinement