2C1F

The structure of the family 11 xylanase from Neocallimastix patriciarum


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
10.1M CDCL2, 0.1M SODIUM ACETATE AND 30% V/V PEG400
Crystal Properties
Matthews coefficientSolvent content
2.855

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 117.336α = 90
b = 117.336β = 90
c = 117.336γ = 90
Symmetry
Space GroupI 2 3

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU IMAGE PLATEMIRRORS2004-04-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU

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
12.137.0496.80.097.377.491535726
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)
12.12.2182.50.362.072.87

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 1F5J2.183.051535776696.80.1680.1660.205RANDOM17.2
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.953
r_dihedral_angle_4_deg26.111
r_dihedral_angle_3_deg14.314
r_dihedral_angle_1_deg7.212
r_scangle_it2.101
r_scbond_it1.454
r_angle_refined_deg1.218
r_mcangle_it0.863
r_mcbond_it0.789
r_symmetry_vdw_refined0.272
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.953
r_dihedral_angle_4_deg26.111
r_dihedral_angle_3_deg14.314
r_dihedral_angle_1_deg7.212
r_scangle_it2.101
r_scbond_it1.454
r_angle_refined_deg1.218
r_mcangle_it0.863
r_mcbond_it0.789
r_symmetry_vdw_refined0.272
r_symmetry_hbond_refined0.238
r_xyhbond_nbd_refined0.204
r_nbd_refined0.183
r_nbtor_refined0.182
r_chiral_restr0.075
r_bond_refined_d0.009
r_gen_planes_refined0.004
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 Atoms1718
Nucleic Acid Atoms
Solvent Atoms173
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing