9HYQ | pdb_00009hyq

BT984 a GH139 rhamnogalacturonan II exo-a-1,2-(2-Omethyl)-fucosidase


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
in silico modelRoseTTAFoldUnpublished structure

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29520 % PEG 3000 0.1 M Tris pH8.5 10 mg/ml
Crystal Properties
Matthews coefficientSolvent content
2.652.69

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 101.201α = 90
b = 138.322β = 90
c = 195.53γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER X 16M2015-01-25MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I04-10.9795DiamondI04-1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)CC (Half)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
12.747.47898.90.99710.43.375053
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.72.760.5021.3

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.747.47875016373698.6330.220.21820.22160.25570.256276.237
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]
-5.108-6.8511.958
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.997
r_dihedral_angle_6_deg14.23
r_lrange_it11.478
r_lrange_other11.478
r_mcangle_it8.7
r_mcangle_other8.7
r_scangle_it8.68
r_scangle_other8.679
r_dihedral_angle_2_deg8.673
r_dihedral_angle_1_deg6.968
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg15.997
r_dihedral_angle_6_deg14.23
r_lrange_it11.478
r_lrange_other11.478
r_mcangle_it8.7
r_mcangle_other8.7
r_scangle_it8.68
r_scangle_other8.679
r_dihedral_angle_2_deg8.673
r_dihedral_angle_1_deg6.968
r_mcbond_it5.664
r_mcbond_other5.662
r_scbond_it5.454
r_scbond_other5.454
r_angle_refined_deg1.4
r_angle_other_deg0.504
r_symmetry_xyhbond_nbd_refined0.344
r_xyhbond_nbd_other0.251
r_nbd_other0.249
r_nbd_refined0.221
r_symmetry_nbd_other0.2
r_nbtor_refined0.188
r_symmetry_nbd_refined0.181
r_xyhbond_nbd_refined0.146
r_ncsr_local_group_10.089
r_symmetry_nbtor_other0.081
r_chiral_restr0.07
r_symmetry_xyhbond_nbd_other0.049
r_bond_refined_d0.005
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12169
Nucleic Acid Atoms
Solvent Atoms12
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
PHASERphasing