2VX6

CELLVIBRIO JAPONICUS MANNANASE CJMAN26C Gal1Man4-BOUND FORM


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1J9YPDB ENTRY 1J9Y

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.3759.37

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.529α = 90
b = 84.529β = 90
c = 244.322γ = 120
Symmetry
Space GroupP 61 2 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID23-1ESRFID23-1

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
11.572099.40.0638.411.3726912
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)
11.571.6399.30.2510.411

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 1J9Y1.5710.5368731365299.650.110020.108610.13672RANDOM9.167
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]
-0.04-0.02-0.040.06
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.195
r_dihedral_angle_4_deg15.548
r_dihedral_angle_3_deg11.514
r_scangle_it6.825
r_scbond_it6.794
r_dihedral_angle_1_deg5.709
r_mcangle_it2.435
r_angle_other_deg1.998
r_mcbond_it1.574
r_angle_refined_deg1.41
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.195
r_dihedral_angle_4_deg15.548
r_dihedral_angle_3_deg11.514
r_scangle_it6.825
r_scbond_it6.794
r_dihedral_angle_1_deg5.709
r_mcangle_it2.435
r_angle_other_deg1.998
r_mcbond_it1.574
r_angle_refined_deg1.41
r_chiral_restr0.088
r_bond_refined_d0.011
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
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_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 Atoms2927
Nucleic Acid Atoms
Solvent Atoms693
Heterogen Atoms58

Software

Software
Software NamePurpose
REFMACrefinement
MOLREPphasing