2WHK

Structure of Bacillus subtilis mannanase man26


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GW1PDB ENTRY 1GW1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.535% PEG8K, 0.2M NA ACETATE, 0.1M TRIS PH 7 TO 8
Crystal Properties
Matthews coefficientSolvent content
2.551

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 67.498α = 90
b = 67.498β = 90
c = 72.966γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-4ESRFID14-4

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
11.7201000.0544740383
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)
11.71.76990.127.11.6

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 1GW11.719.4838734204699.70.1720.170.204RANDOM16.3
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]
-0.03-0.02-0.030.05
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.554
r_dihedral_angle_4_deg17.175
r_dihedral_angle_3_deg13.112
r_dihedral_angle_1_deg5.914
r_sphericity_free3.451
r_sphericity_bonded2.555
r_scangle_it2.471
r_scbond_it1.634
r_mcangle_it1.276
r_angle_other_deg1.177
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.554
r_dihedral_angle_4_deg17.175
r_dihedral_angle_3_deg13.112
r_dihedral_angle_1_deg5.914
r_sphericity_free3.451
r_sphericity_bonded2.555
r_scangle_it2.471
r_scbond_it1.634
r_mcangle_it1.276
r_angle_other_deg1.177
r_angle_refined_deg1.099
r_rigid_bond_restr1.086
r_mcbond_it0.695
r_mcbond_other0.295
r_chiral_restr0.088
r_bond_refined_d0.007
r_gen_planes_refined0.004
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
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2666
Nucleic Acid Atoms
Solvent Atoms354
Heterogen Atoms23

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing