8FHC | pdb_00008fhc

Protein 41 with aldehyde deformylating oxidase activity from Gamma proteobacterium


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP29827% PEG 3350, 200 mM NaCl, 1.5 mM cholalic acid sodium salt, 100 mM imidazole
Crystal Properties
Matthews coefficientSolvent content
2.3247

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 48.296α = 90
b = 85.711β = 90
c = 112.558γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100PIXELDECTRIS PILATUS 6M2017-08-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONSSRL BEAMLINE BL9-20.97946SSRLBL9-2

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
12.09739.44399.60.1070.1130.0350.998169.928065
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)
12.12.160.5790.6140.1980.9269.2

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)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTFREE R-VALUE2.09739.44328008138499.460.1970.19540.210.23620.250.0525.821
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]
-3.0882.9350.153
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.069
r_dihedral_angle_6_deg14.227
r_dihedral_angle_2_deg6.302
r_lrange_it5.829
r_lrange_other5.739
r_dihedral_angle_1_deg5.104
r_scangle_it4.488
r_scangle_other4.488
r_scbond_it2.909
r_scbond_other2.909
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_3_deg16.069
r_dihedral_angle_6_deg14.227
r_dihedral_angle_2_deg6.302
r_lrange_it5.829
r_lrange_other5.739
r_dihedral_angle_1_deg5.104
r_scangle_it4.488
r_scangle_other4.488
r_scbond_it2.909
r_scbond_other2.909
r_mcangle_it2.671
r_mcangle_other2.671
r_mcbond_it1.812
r_mcbond_other1.81
r_angle_refined_deg1.356
r_angle_other_deg0.444
r_nbd_refined0.22
r_symmetry_nbd_refined0.206
r_xyhbond_nbd_refined0.197
r_nbd_other0.186
r_nbtor_refined0.18
r_symmetry_nbd_other0.176
r_symmetry_xyhbond_nbd_refined0.099
r_symmetry_nbtor_other0.075
r_chiral_restr0.064
r_metal_ion_refined0.037
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 Atoms3486
Nucleic Acid Atoms
Solvent Atoms198
Heterogen Atoms45

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing