6ZPX | pdb_00006zpx

Structure of Unliganded MgGH51 a-L-Arabinofuranosidase Crystal Type 1


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529310 mg/mL MgGH51 in 10 mM NaOAc, pH 5.5, 100 mM NaCl mixed 2:1 with 20% PEG 3350, 0.1 M Bis-Tris-HCl, pH 6.5, 0.2 M NaNO3
Crystal Properties
Matthews coefficientSolvent content
2.8256.31

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 59.98α = 90
b = 65.801β = 90
c = 193.12γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2019-09-14MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

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
11.382.281000.0350.9986.97.8188207
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)
11.31.3299.70.4220.7786

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE6ZPS1.362.362188071938499.860.180.17810.180.21740.2118.808
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]
3.335-1.622-1.713
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.442
r_dihedral_angle_4_deg16.759
r_dihedral_angle_3_deg12.423
r_dihedral_angle_1_deg7.365
r_rigid_bond_restr3.843
r_scangle_other2.801
r_scangle_it2.797
r_lrange_it2.673
r_scbond_it2.622
r_scbond_other2.622
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg34.442
r_dihedral_angle_4_deg16.759
r_dihedral_angle_3_deg12.423
r_dihedral_angle_1_deg7.365
r_rigid_bond_restr3.843
r_scangle_other2.801
r_scangle_it2.797
r_lrange_it2.673
r_scbond_it2.622
r_scbond_other2.622
r_lrange_other2.552
r_mcangle_other2.084
r_mcangle_it2.077
r_angle_refined_deg1.899
r_mcbond_it1.834
r_mcbond_other1.818
r_angle_other_deg1.593
r_nbd_refined0.202
r_symmetry_nbd_other0.189
r_nbtor_refined0.18
r_symmetry_xyhbond_nbd_refined0.156
r_xyhbond_nbd_refined0.136
r_chiral_restr0.118
r_nbd_other0.114
r_symmetry_xyhbond_nbd_other0.095
r_symmetry_nbtor_other0.087
r_symmetry_nbd_refined0.049
r_bond_refined_d0.016
r_gen_planes_refined0.015
r_gen_planes_other0.002
r_bond_other_d0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4769
Nucleic Acid Atoms
Solvent Atoms643
Heterogen Atoms124

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
DIALSdata scaling
MOLREPphasing