6ZPS | pdb_00006zps

Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 3 Collected at 2.75 A


X-RAY DIFFRACTION

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
3.3763.47

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 84.171α = 90
b = 84.171β = 90
c = 257.347γ = 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 I232.755DiamondI23

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
11.79257.3584.40.0120.99935.170.274070
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)
11.791.890.50.1420.915.721.5

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 DIFFRACTIONSADFREE R-VALUE1.79580.12873955357084.5290.1450.14380.14380.17840.178519.521
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]
0.3890.389-0.778
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.417
r_dihedral_angle_4_deg16.855
r_dihedral_angle_3_deg11.996
r_dihedral_angle_1_deg7.071
r_lrange_it5.181
r_lrange_other4.853
r_scangle_it4.009
r_scangle_other4.008
r_scbond_it2.806
r_scbond_other2.805
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.417
r_dihedral_angle_4_deg16.855
r_dihedral_angle_3_deg11.996
r_dihedral_angle_1_deg7.071
r_lrange_it5.181
r_lrange_other4.853
r_scangle_it4.009
r_scangle_other4.008
r_scbond_it2.806
r_scbond_other2.805
r_mcangle_it2.137
r_mcangle_other2.137
r_angle_refined_deg1.792
r_mcbond_it1.588
r_mcbond_other1.585
r_angle_other_deg1.514
r_symmetry_xyhbond_nbd_other0.481
r_xyhbond_nbd_refined0.282
r_nbd_refined0.231
r_nbd_other0.196
r_symmetry_xyhbond_nbd_refined0.184
r_symmetry_nbd_other0.183
r_nbtor_refined0.174
r_symmetry_nbd_refined0.114
r_chiral_restr0.097
r_symmetry_nbtor_other0.084
r_bond_refined_d0.013
r_gen_planes_refined0.012
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4790
Nucleic Acid Atoms
Solvent Atoms751
Heterogen Atoms285

Software

Software
Software NamePurpose
REFMACrefinement
xia2data processing
Aimlessdata scaling
CRANK2phasing