2X34

Structure of a polyisoprenoid binding domain from Saccharophagus degradans implicated in plant cell wall breakdown


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
15.542% PEG600, 0.2M IMIDAZOL-MALATE PH 5.5
Crystal Properties
Matthews coefficientSolvent content
2.448.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 62.979α = 90
b = 64.964β = 90
c = 84.191γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120CCDADSC QUANTUM 315r2008-07-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSOLEIL BEAMLINE PROXIMA 1SOLEILPROXIMA 1

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
11.95199.80.1214.47278562
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)
11.9299.10.415.57.1

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 DIFFRACTIONSADTHROUGHOUTNONE1.951.4326470139999.90.1780.1750.223RANDOM6.89
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]
-0.70.7
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.125
r_dihedral_angle_4_deg13.93
r_dihedral_angle_3_deg11.089
r_dihedral_angle_1_deg5.903
r_scangle_it3.204
r_scbond_it2.092
r_angle_refined_deg1.479
r_mcangle_it1.263
r_angle_other_deg1.007
r_mcbond_it0.695
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.125
r_dihedral_angle_4_deg13.93
r_dihedral_angle_3_deg11.089
r_dihedral_angle_1_deg5.903
r_scangle_it3.204
r_scbond_it2.092
r_angle_refined_deg1.479
r_mcangle_it1.263
r_angle_other_deg1.007
r_mcbond_it0.695
r_mcbond_other0.156
r_chiral_restr0.081
r_bond_refined_d0.013
r_gen_planes_refined0.005
r_bond_other_d0.001
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_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 Atoms2618
Nucleic Acid Atoms
Solvent Atoms364
Heterogen Atoms106

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
AutoSolphasing