2WHM | pdb_00002whm

Cellvibrio japonicus Man26A E121A and E320G double mutant in complex with mannobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1GW1PDB ENTRY 1GW1

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
17.5100MMTRIS PH7, 26% MEONOMETHYLETHER PEG550, 3MM ZNSO4, pH 7.5
Crystal Properties
Matthews coefficientSolvent content
2.755

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 93.177α = 90
b = 93.177β = 90
c = 53.78γ = 90
Symmetry
Space GroupP 41

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCDMSINGLE 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
11.5301000.04533.773813
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)
11.51.551000.275.23.7

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 DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1GW11.519.9870068371199.90.1450.1440.140.1650.16RANDOM18.25
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]
-0.01
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg33.584
r_dihedral_angle_4_deg13.042
r_dihedral_angle_3_deg10.965
r_dihedral_angle_1_deg5.594
r_sphericity_free4.734
r_scangle_it3.521
r_sphericity_bonded3.102
r_scbond_it2.395
r_mcangle_it1.723
r_rigid_bond_restr1.361
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3013
Nucleic Acid Atoms
Solvent Atoms423
Heterogen Atoms41

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling