4IPM

Crystal structure of a GH7 family cellobiohydrolase from Limnoria quadripunctata in complex with thiocellobiose


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4GWA 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.5289100mM sodium acetate pH 4.5, 500mM CaCl2, 15% (w/v) PEG 6000, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1442.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 47.49α = 90
b = 79.78β = 90
c = 105.16γ = 90
Symmetry
Space GroupP 2 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2012-10-31MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I040.9795DiamondI04

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
11.1463.55996.40.0848.43.7150535140362
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.141.1672.70.6360.4821.32.35172

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT4GWA1.1423150535140221704796.070.12340.12170.1551RANDOM12.7332
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]
0.02-0.020.01
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free59.449
r_dihedral_angle_2_deg32.308
r_dihedral_angle_4_deg22.078
r_sphericity_bonded16.264
r_dihedral_angle_3_deg12.036
r_dihedral_angle_1_deg6.595
r_rigid_bond_restr6.196
r_angle_refined_deg2.025
r_angle_other_deg0.958
r_chiral_restr0.138
RMS Deviations
KeyRefinement Restraint Deviation
r_sphericity_free59.449
r_dihedral_angle_2_deg32.308
r_dihedral_angle_4_deg22.078
r_sphericity_bonded16.264
r_dihedral_angle_3_deg12.036
r_dihedral_angle_1_deg6.595
r_rigid_bond_restr6.196
r_angle_refined_deg2.025
r_angle_other_deg0.958
r_chiral_restr0.138
r_bond_refined_d0.022
r_gen_planes_refined0.012
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3258
Nucleic Acid Atoms
Solvent Atoms687
Heterogen Atoms28

Software

Software
Software NamePurpose
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction
GDAdata collection