2V5C | pdb_00002v5c

Family 84 glycoside hydrolase from Clostridium perfringens, 2.1 Angstrom structure


X-RAY DIFFRACTION

Crystallization

Crystal Properties
Matthews coefficientSolvent content
2.5952.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 130.385α = 90
b = 150.046β = 90
c = 155.428γ = 90
Symmetry
Space GroupI 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray113.15 MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODE

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
12.1105.4199.90.116.14857522

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONOTHERTHROUGHOUTNONE2.1105.4184080444099.70.1980.1950.190.2550.25RANDOM31.1
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]
1.19-0.06-1.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg39.427
r_dihedral_angle_3_deg16.963
r_dihedral_angle_4_deg14.921
r_dihedral_angle_1_deg7.187
r_scangle_it2.51
r_scbond_it1.526
r_angle_refined_deg1.389
r_mcangle_it0.979
r_mcbond_it0.514
r_nbtor_refined0.3
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms9238
Nucleic Acid Atoms
Solvent Atoms1191
Heterogen Atoms31

Software

Software
Software NamePurpose
REFMACrefinement