5JP6

Bdellovibrio bacteriovorus peptidoglycan deacetylase Bd3279


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C1G 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6.52980.1M Na cacodylate pH 6.5 0.2M Mg acetate 20% w/v/ PEG 8000
Crystal Properties
Matthews coefficientSolvent content
3.463.79

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 112.434α = 90
b = 112.434β = 90
c = 79.859γ = 120
Symmetry
Space GroupP 61

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-03-21MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.97950DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
11.597.3799.925.11491430

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 REPLACEMENTTHROUGHOUT2C1G1.597.3786803458199.810.14580.14480.1668RANDOM29.028
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]
0.060.030.06-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.609
r_dihedral_angle_2_deg34.399
r_sphericity_bonded15.856
r_dihedral_angle_3_deg12.687
r_dihedral_angle_4_deg12.221
r_dihedral_angle_1_deg5.558
r_rigid_bond_restr4.286
r_mcangle_it3.398
r_mcbond_it2.825
r_mcbond_other2.787
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free34.609
r_dihedral_angle_2_deg34.399
r_sphericity_bonded15.856
r_dihedral_angle_3_deg12.687
r_dihedral_angle_4_deg12.221
r_dihedral_angle_1_deg5.558
r_rigid_bond_restr4.286
r_mcangle_it3.398
r_mcbond_it2.825
r_mcbond_other2.787
r_angle_refined_deg1.552
r_angle_other_deg0.863
r_chiral_restr0.096
r_bond_refined_d0.014
r_gen_planes_refined0.008
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2689
Nucleic Acid Atoms
Solvent Atoms265
Heterogen Atoms2

Software

Software
Software NamePurpose
SCALAdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
PHASERphasing