9FBS | pdb_00009fbs

Deletion mutant of chitinase MmChi60


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 4W5Zsimilar content

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP829320% (w/v) PEG 4000, 0.4 M MgCl2, 0.1 M Tris pH 8.0
Crystal Properties
Matthews coefficientSolvent content
2.2445.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 50.764α = 90
b = 74.009β = 90
c = 172.538γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS3 2Mfocusing mirrors2017-10-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.9184BESSY14.1

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim 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
12.355099.30.1440.1520.99712.79.413787
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.352.5960.9611.0150.7622.249.6

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (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-VALUE2.35443.1341378682899.2660.1910.18590.19790.26550.273542.173
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]
-0.131-0.0180.149
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.897
r_dihedral_angle_3_deg14.927
r_lrange_it7.379
r_lrange_other7.376
r_dihedral_angle_1_deg6.596
r_scangle_it5.736
r_scangle_other5.735
r_mcangle_it4.671
r_mcangle_other4.671
r_dihedral_angle_2_deg3.947
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg15.897
r_dihedral_angle_3_deg14.927
r_lrange_it7.379
r_lrange_other7.376
r_dihedral_angle_1_deg6.596
r_scangle_it5.736
r_scangle_other5.735
r_mcangle_it4.671
r_mcangle_other4.671
r_dihedral_angle_2_deg3.947
r_scbond_it3.732
r_scbond_other3.731
r_mcbond_it3.148
r_mcbond_other3.148
r_angle_refined_deg1.356
r_angle_other_deg0.496
r_nbd_refined0.22
r_symmetry_nbd_other0.193
r_nbtor_refined0.182
r_symmetry_nbd_refined0.16
r_nbd_other0.147
r_symmetry_xyhbond_nbd_refined0.143
r_xyhbond_nbd_refined0.117
r_metal_ion_refined0.077
r_symmetry_nbtor_other0.076
r_chiral_restr0.068
r_bond_refined_d0.006
r_gen_planes_refined0.006
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2551
Nucleic Acid Atoms
Solvent Atoms76
Heterogen Atoms2

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing