2CNC

Family 10 xylanase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1UR1PDB ENTRY 1UR1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
16.50.35 M MGCL2, 0.1 M TRIS, PH 6.5, 30% PEG 4000, 5% PEG 400
Crystal Properties
Matthews coefficientSolvent content
3.564.2

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 46.904α = 90
b = 67.365β = 90
c = 105.156γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray110IMAGE PLATERIGAKU IMAGE PLATEMIRRORSMSINGLE 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
12.438.49860.0714.22.1114652
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)
12.42.53840.24.12

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 1UR12.456.71084758884.20.1610.1550.273RANDOM11.29
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]
-0.020.27-0.25
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.445
r_dihedral_angle_3_deg18.265
r_dihedral_angle_4_deg18.224
r_dihedral_angle_1_deg8.24
r_scangle_it3.959
r_scbond_it2.667
r_angle_refined_deg2.157
r_mcangle_it1.593
r_mcbond_it0.994
r_symmetry_hbond_refined0.343
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.445
r_dihedral_angle_3_deg18.265
r_dihedral_angle_4_deg18.224
r_dihedral_angle_1_deg8.24
r_scangle_it3.959
r_scbond_it2.667
r_angle_refined_deg2.157
r_mcangle_it1.593
r_mcbond_it0.994
r_symmetry_hbond_refined0.343
r_nbtor_refined0.318
r_symmetry_vdw_refined0.301
r_nbd_refined0.237
r_xyhbond_nbd_refined0.229
r_chiral_restr0.15
r_bond_refined_d0.023
r_gen_planes_refined0.009
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 Atoms2833
Nucleic Acid Atoms
Solvent Atoms298
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing