2V38

Family 5 endoglucanase Cel5A from Bacillus agaradhaerens in complex with cellobio-derived noeuromycin


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OCQPDB ENTRY 1OCQ

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
110 MG/ML PROTEIN. 1.5-1.8 M AMMONIUM SULPHATE. 25% GLYCEROL AS CRYO.
Crystal Properties
Matthews coefficientSolvent content
2.243

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 54.861α = 90
b = 69.595β = 90
c = 76.719γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDSAGITALLY FOCUSING GE(220) AND A MULTILAYER2006-11-09MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-1ESRFID14-1

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
11.52099.90.0628.55.547760
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)
11.51.551000.266.35.4

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 1OCQ1.551.5745273241699.70.1130.1110.143RANDOM8.36
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]
1.28-0.66-0.62
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.088
r_dihedral_angle_4_deg18.017
r_dihedral_angle_3_deg11.563
r_dihedral_angle_1_deg6.192
r_scangle_it3.557
r_scbond_it2.556
r_mcangle_it1.598
r_angle_refined_deg1.436
r_mcbond_it1.3
r_angle_other_deg0.976
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.088
r_dihedral_angle_4_deg18.017
r_dihedral_angle_3_deg11.563
r_dihedral_angle_1_deg6.192
r_scangle_it3.557
r_scbond_it2.556
r_mcangle_it1.598
r_angle_refined_deg1.436
r_mcbond_it1.3
r_angle_other_deg0.976
r_symmetry_vdw_refined0.262
r_symmetry_vdw_other0.237
r_nbd_refined0.206
r_nbd_other0.198
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.157
r_symmetry_hbond_refined0.105
r_chiral_restr0.096
r_nbtor_other0.088
r_bond_refined_d0.012
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_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
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2381
Nucleic Acid Atoms
Solvent Atoms409
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
REFMACphasing