6ZPV

Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 3


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 6ZPS 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP29310 mg/mL MgGH51 in 10 mM NaOAc pH 5.5, 100 mM NaCl mixed 2:1 with 1.8 M (NH4)2SO4, 0.1 M NaOAc, pH 5-6, 35% glycerol
Crystal Properties
Matthews coefficientSolvent content
3.3463.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 83.953α = 90
b = 83.953β = 90
c = 256.589γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80PIXELDECTRIS PILATUS 2M2019-12-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I231.3775DiamondI23

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)Rpim I (All)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
11.285.531000.011127.233285059
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.21.221000.430.4211.825.1

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-WorkR-FreeMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6ZPS1.279.9182848611414999.9710.1210.11990.14415.41
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]
0.1670.167-0.334
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.969
r_dihedral_angle_4_deg14.656
r_dihedral_angle_3_deg11.45
r_rigid_bond_restr7.532
r_dihedral_angle_1_deg7.057
r_scbond_it4.656
r_scbond_other4.655
r_scangle_it4.425
r_scangle_other4.425
r_lrange_it3.806
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.969
r_dihedral_angle_4_deg14.656
r_dihedral_angle_3_deg11.45
r_rigid_bond_restr7.532
r_dihedral_angle_1_deg7.057
r_scbond_it4.656
r_scbond_other4.655
r_scangle_it4.425
r_scangle_other4.425
r_lrange_it3.806
r_lrange_other3.681
r_angle_refined_deg2.073
r_angle_other_deg1.647
r_mcangle_it1.327
r_mcangle_other1.327
r_mcbond_it1.159
r_mcbond_other1.153
r_symmetry_xyhbond_nbd_other0.319
r_nbd_other0.236
r_nbd_refined0.233
r_xyhbond_nbd_refined0.23
r_symmetry_nbd_other0.19
r_symmetry_xyhbond_nbd_refined0.185
r_nbtor_refined0.181
r_symmetry_nbd_refined0.174
r_chiral_restr0.13
r_symmetry_nbtor_other0.09
r_xyhbond_nbd_other0.035
r_bond_refined_d0.018
r_gen_planes_refined0.013
r_gen_planes_other0.003
r_bond_other_d0.002
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4788
Nucleic Acid Atoms
Solvent Atoms1082
Heterogen Atoms264

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
Aimlessdata scaling
MOLREPphasing