2CC0

Family 4 carbohydrate esterase from Streptomyces lividans in complex with acetate


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2C71PDB ENTRY 2C71

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
14.57-13% PEG 4K, 0.2 M KBR, 0.1 M NAAC, PH 4.5. PROTEIN 20 MG/ML.
Crystal Properties
Matthews coefficientSolvent content
2.0539.39

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 95.538α = 90
b = 47.905β = 90
c = 89.842γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDTOROIDAL MIRRORMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID29ESRFID29

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
11.640980.05173.451014
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)
11.61.66910.2642.8

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-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 2C711.665.6551014273498.10.1520.150.188RANDOM16.32
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]
-0.460.110.35
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.422
r_dihedral_angle_4_deg17.809
r_dihedral_angle_3_deg12.414
r_dihedral_angle_1_deg11.255
r_sphericity_free5.219
r_sphericity_bonded4.223
r_scangle_it3.682
r_scbond_it2.581
r_mcangle_it1.785
r_rigid_bond_restr1.471
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg37.422
r_dihedral_angle_4_deg17.809
r_dihedral_angle_3_deg12.414
r_dihedral_angle_1_deg11.255
r_sphericity_free5.219
r_sphericity_bonded4.223
r_scangle_it3.682
r_scbond_it2.581
r_mcangle_it1.785
r_rigid_bond_restr1.471
r_angle_refined_deg1.447
r_mcbond_it1.203
r_nbtor_refined0.303
r_nbd_refined0.199
r_symmetry_vdw_refined0.184
r_symmetry_hbond_refined0.154
r_xyhbond_nbd_refined0.144
r_chiral_restr0.099
r_bond_refined_d0.013
r_metal_ion_refined0.012
r_gen_planes_refined0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2857
Nucleic Acid Atoms
Solvent Atoms564
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing