5GZH

Endo-beta-1,2-glucanase from Chitinophaga pinensis - ligand free form


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP2980.1 M ammonium iodide, 7% PEG 3350
Crystal Properties
Matthews coefficientSolvent content
2.9558.4

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.965α = 90
b = 90.965β = 90
c = 124.086γ = 120
Symmetry
Space GroupP 31

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 2102015-06-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONPHOTON FACTORY BEAMLINE AR-NW12A1.0000Photon FactoryAR-NW12A

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
11.850990.09821.35.310556619.7
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.831000.6820.8232.35.6

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 REPLACEMENTTHROUGHOUT3EU81.848.74100115531798.990.16990.168070.20437RANDOM28.34
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_deg37.868
r_dihedral_angle_4_deg14.169
r_dihedral_angle_3_deg13.133
r_dihedral_angle_1_deg6.242
r_long_range_B_refined5.614
r_long_range_B_other5.614
r_scangle_other4.392
r_scbond_it3.104
r_scbond_other3.104
r_mcangle_it2.959
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.868
r_dihedral_angle_4_deg14.169
r_dihedral_angle_3_deg13.133
r_dihedral_angle_1_deg6.242
r_long_range_B_refined5.614
r_long_range_B_other5.614
r_scangle_other4.392
r_scbond_it3.104
r_scbond_other3.104
r_mcangle_it2.959
r_mcangle_other2.958
r_mcbond_it2.387
r_mcbond_other2.387
r_angle_refined_deg1.852
r_angle_other_deg1.098
r_chiral_restr0.126
r_bond_refined_d0.02
r_gen_planes_refined0.012
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_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6934
Nucleic Acid Atoms
Solvent Atoms639
Heterogen Atoms70

Software

Software
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
MOLREPphasing