7QJR | pdb_00007qjr

Crystal structure of cutinase 1 from Thermobifida fusca DSM44342 (703)


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4CG1 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP28120 % PEG 3350, 0.02 M sodium / potassium phosphate, 0.1 M Bis-Tris propane pH 6.5
Crystal Properties
Matthews coefficientSolvent content
2.5752.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 71.68α = 90
b = 71.68β = 90
c = 102.52γ = 120
Symmetry
Space GroupP 32 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 6M2020-01-26MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I240.9686DiamondI24

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)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
11.5162.081000.1150.0270.99914.519.448462
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.511.541003.6820.8520.350.9

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)Mean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE4CG11.5162.07748416230799.9960.1560.15420.170.18550.1925.381
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]
0.0410.0210.041-0.133
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.004
r_dihedral_angle_4_deg17.457
r_dihedral_angle_3_deg11.068
r_dihedral_angle_1_deg6.651
r_lrange_it5.624
r_lrange_other5.516
r_scangle_it3.943
r_scangle_other3.941
r_scbond_other2.627
r_scbond_it2.625
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg27.004
r_dihedral_angle_4_deg17.457
r_dihedral_angle_3_deg11.068
r_dihedral_angle_1_deg6.651
r_lrange_it5.624
r_lrange_other5.516
r_scangle_it3.943
r_scangle_other3.941
r_scbond_other2.627
r_scbond_it2.625
r_mcangle_it2.431
r_mcangle_other2.43
r_angle_refined_deg2.044
r_mcbond_it1.617
r_angle_other_deg1.614
r_mcbond_other1.608
r_nbd_refined0.222
r_symmetry_xyhbond_nbd_refined0.19
r_xyhbond_nbd_refined0.189
r_symmetry_nbd_other0.182
r_nbd_other0.18
r_symmetry_nbd_refined0.179
r_nbtor_refined0.177
r_symmetry_xyhbond_nbd_other0.108
r_chiral_restr0.107
r_symmetry_nbtor_other0.089
r_bond_refined_d0.017
r_gen_planes_refined0.013
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2018
Nucleic Acid Atoms
Solvent Atoms222
Heterogen Atoms10

Software

Software
Software NamePurpose
REFMACrefinement
xia2data reduction
xia2data scaling
MOLREPphasing