4HAP

Crystal Structure of a GH7 family cellobiohydrolase from Limnoria quadripunctata in complex with cellobiose


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52890.1M Sodium Acetate, 15% w/v PEG 6000, 0.5M CaCl2, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 289K
Crystal Properties
Matthews coefficientSolvent content
2.1843.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 52.26α = 94.26
b = 54.19β = 96.02
c = 72.45γ = 94.99
Symmetry
Space GroupP 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2012-05-06MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I020.9173DiamondI02

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym 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
11.671.79593.40.1137.63.39674896748
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.61.6991.90.5950.5950.7210.41.23.113891

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 REPLACEMENTTHROUGHOUT4GWA1.639.99824896745484693.430.14670.14440.1906RANDOM14.5747
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.348
r_dihedral_angle_4_deg23.012
r_dihedral_angle_3_deg13.388
r_dihedral_angle_1_deg6.63
r_angle_refined_deg2.009
r_angle_other_deg0.945
r_chiral_restr0.129
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.002
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg35.348
r_dihedral_angle_4_deg23.012
r_dihedral_angle_3_deg13.388
r_dihedral_angle_1_deg6.63
r_angle_refined_deg2.009
r_angle_other_deg0.945
r_chiral_restr0.129
r_bond_refined_d0.021
r_gen_planes_refined0.011
r_bond_other_d0.002
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms6514
Nucleic Acid Atoms
Solvent Atoms1261
Heterogen Atoms59

Software

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