2JEM

Native family 12 xyloglucanase from Bacillus licheniformis


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1NLRPDB ENTRY 1NLR

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.510% W/V PEG4000, 0.05 M MGCL2, 0.1 M BIS-TRIS, PH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.448

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.748α = 90
b = 78.133β = 109.8
c = 69.103γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray120IMAGE PLATEMARRESEARCHMULTILAYERMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU200

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
11.782094.30.0427.74.144098
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)
11.781.8281.50.254.13

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 1NLR1.7864.5542703137294.40.1560.1550.2RANDOM16.21
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]
-0.02-0.070.77-0.79
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.342
r_dihedral_angle_3_deg12.012
r_dihedral_angle_4_deg9.471
r_dihedral_angle_1_deg7.08
r_scangle_it2.698
r_scbond_it1.893
r_angle_refined_deg1.36
r_mcangle_it1.196
r_mcbond_it0.77
r_nbtor_refined0.304
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.342
r_dihedral_angle_3_deg12.012
r_dihedral_angle_4_deg9.471
r_dihedral_angle_1_deg7.08
r_scangle_it2.698
r_scbond_it1.893
r_angle_refined_deg1.36
r_mcangle_it1.196
r_mcbond_it0.77
r_nbtor_refined0.304
r_nbd_refined0.199
r_symmetry_vdw_refined0.191
r_xyhbond_nbd_refined0.127
r_symmetry_hbond_refined0.124
r_chiral_restr0.103
r_bond_refined_d0.013
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 Atoms3694
Nucleic Acid Atoms
Solvent Atoms709
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling