8BNW | pdb_00008bnw

X-ray structure of the CeuE Homologue from Parageobacillus thermoglucosidasius - apo form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 8BF6 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP6.529317% PEG 3350; 0.1M MES, pH 6.5, 0.1M MgAc; Cryo- EthGl
Crystal Properties
Matthews coefficientSolvent content
2.2645.51

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.369α = 90
b = 118.433β = 90
c = 141.046γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS EIGER2 X 16M2021-02-03MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONDIAMOND BEAMLINE I030.976300DiamondI03

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)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
12.1370.6231000.0690.0740.028117.812.717078
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.132.193.2723.5431.3520.37712.9

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-VALUE8BF62.13370.6231704586299.930.2240.22160.230.26610.2776.498
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]
1.5720.088-1.66
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.985
r_dihedral_angle_6_deg14.585
r_lrange_it10.572
r_lrange_other10.572
r_scangle_it8.103
r_dihedral_angle_1_deg8.1
r_scangle_other7.825
r_mcangle_it6.954
r_mcangle_other6.952
r_scbond_it5.681
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg17.985
r_dihedral_angle_6_deg14.585
r_lrange_it10.572
r_lrange_other10.572
r_scangle_it8.103
r_dihedral_angle_1_deg8.1
r_scangle_other7.825
r_mcangle_it6.954
r_mcangle_other6.952
r_scbond_it5.681
r_scbond_other5.414
r_mcbond_it4.962
r_mcbond_other4.96
r_dihedral_angle_2_deg2.305
r_angle_refined_deg1.246
r_symmetry_nbd_refined0.447
r_angle_other_deg0.388
r_symmetry_metal_ion_refined0.324
r_symmetry_xyhbond_nbd_refined0.29
r_nbd_refined0.234
r_nbd_other0.224
r_xyhbond_nbd_refined0.207
r_symmetry_nbd_other0.189
r_nbtor_refined0.179
r_symmetry_nbtor_other0.08
r_symmetry_xyhbond_nbd_other0.07
r_chiral_restr0.052
r_bond_refined_d0.008
r_gen_planes_refined0.005
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms2167
Nucleic Acid Atoms
Solvent Atoms9
Heterogen Atoms15

Software

Software
Software NamePurpose
REFMACrefinement
REFMACrefinement
DIALSdata reduction
Aimlessdata scaling
MOLREPphasing