2JEQ

Family 5 xyloglucanase from Paenibacillus pabuli in complex with ligand


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2JEPPDB ENTRY 2JEP

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18.525% PEG 3350, 0.2 M MGCL2, 0.1 M TRIS, PH 8.5
Crystal Properties
Matthews coefficientSolvent content
1.832.1

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 85.066α = 90
b = 89.16β = 90
c = 38.705γ = 90
Symmetry
Space GroupP 21 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDSAGITALLY FOCUSING GE(220) AND A MULTILAYER2003-08-04MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.955098.80.1113.34.222170
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)
11.952.0291.70.4234.1

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2JEP1.9461.5520757111797.90.1860.1820.26RANDOM21.02
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]
-0.25-1.51.75
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.077
r_dihedral_angle_4_deg19.452
r_dihedral_angle_3_deg14.925
r_dihedral_angle_1_deg6.182
r_scangle_it2.861
r_scbond_it1.947
r_angle_refined_deg1.443
r_mcangle_it1.27
r_mcbond_it0.791
r_nbtor_refined0.314
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.077
r_dihedral_angle_4_deg19.452
r_dihedral_angle_3_deg14.925
r_dihedral_angle_1_deg6.182
r_scangle_it2.861
r_scbond_it1.947
r_angle_refined_deg1.443
r_mcangle_it1.27
r_mcbond_it0.791
r_nbtor_refined0.314
r_symmetry_vdw_refined0.203
r_nbd_refined0.201
r_symmetry_hbond_refined0.163
r_xyhbond_nbd_refined0.156
r_chiral_restr0.097
r_bond_refined_d0.014
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
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 Atoms2843
Nucleic Acid Atoms
Solvent Atoms247
Heterogen Atoms74

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing