9H8I | pdb_00009h8i

Crystallization of B. licheniformis levanase


X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP8.529310% w/v PEG 8000, 20% v/v ethylene glycol and 0.03 M Magnesium chloride, calcium chloride and 0.1 M bicine/Trizma base pH 8.5
Crystal Properties
Matthews coefficientSolvent content
2.8757.11

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 82.586α = 90
b = 82.586β = 90
c = 171.088γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-01-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.9763DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)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
11.574.37597.10.99915.926.185690
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.541.570.6980.639

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-VALUE4fff1.5474.37585314427296.7720.1940.19280.2040.21690.228823.445
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]
-0.132-0.1320.263
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.398
r_dihedral_angle_3_deg12.529
r_lrange_it8.627
r_lrange_other8.626
r_dihedral_angle_1_deg7.197
r_dihedral_angle_2_deg6.503
r_scangle_it6.481
r_scangle_other6.48
r_scbond_it4.193
r_scbond_other4.192
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_6_deg14.398
r_dihedral_angle_3_deg12.529
r_lrange_it8.627
r_lrange_other8.626
r_dihedral_angle_1_deg7.197
r_dihedral_angle_2_deg6.503
r_scangle_it6.481
r_scangle_other6.48
r_scbond_it4.193
r_scbond_other4.192
r_mcangle_other3.709
r_mcangle_it3.705
r_mcbond_it2.533
r_mcbond_other2.509
r_angle_refined_deg1.815
r_angle_other_deg0.63
r_symmetry_nbd_refined0.38
r_nbd_other0.268
r_symmetry_nbd_other0.199
r_nbd_refined0.198
r_nbtor_refined0.183
r_xyhbond_nbd_refined0.135
r_symmetry_xyhbond_nbd_refined0.099
r_chiral_restr0.094
r_metal_ion_refined0.091
r_symmetry_nbtor_other0.086
r_bond_refined_d0.011
r_gen_planes_refined0.01
r_symmetry_metal_ion_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_chiral_restr_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3583
Nucleic Acid Atoms
Solvent Atoms242
Heterogen Atoms32

Software

Software
Software NamePurpose
REFMACrefinement
DIALSdata reduction
MrBUMPphasing
SCALAdata scaling