3M46

The crystal structure of the D73A mutant of glycoside HYDROLASE (FAMILY 31) from Ruminococcus obeum ATCC 29174


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3FFJPDB entry 3FFJ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP5.52890.1M BIS-TRIS, 25% PEG3350, 5mM maltose, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.141.56

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64.182α = 90
b = 122.486β = 108.6
c = 87.46γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315rMirror2010-02-24MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-ID0.97951APS19-ID

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
12.658399.50.1438.83.53653436534
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.652.799.20.7421.453.42001

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB entry 3FFJ2.6682.893468734687182599.030.19220.19220.188740.25788RANDOM37.13
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]
-0.95-0.411.9-1.22
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.667
r_dihedral_angle_3_deg19.8
r_dihedral_angle_4_deg18.227
r_dihedral_angle_1_deg6.81
r_scangle_it3.168
r_scbond_it1.917
r_angle_refined_deg1.535
r_mcangle_it1.239
r_mcbond_it0.628
r_chiral_restr0.107
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.667
r_dihedral_angle_3_deg19.8
r_dihedral_angle_4_deg18.227
r_dihedral_angle_1_deg6.81
r_scangle_it3.168
r_scbond_it1.917
r_angle_refined_deg1.535
r_mcangle_it1.239
r_mcbond_it0.628
r_chiral_restr0.107
r_bond_refined_d0.015
r_gen_planes_refined0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms10654
Nucleic Acid Atoms
Solvent Atoms52
Heterogen Atoms6

Software

Software
Software NamePurpose
SBC-Collectdata collection
MOLREPphasing
HKL-3000phasing
REFMACrefinement
HKL-3000data reduction
HKL-3000data scaling