8FHC | pdb_00008fhc

Protein 41 with aldehyde deformylating oxidase activity from Gamma proteobacterium

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		298	27% PEG 3350, 200 mM NaCl, 1.5 mM cholalic acid sodium salt, 100 mM imidazole

Crystal Properties
Matthews coefficient	Solvent content
2.32	47

Crystal Data

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

Symmetry
Space Group	P 21 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M		2017-08-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.97946	SSRL	BL9-2

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)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.097	39.443	99.6	0.107	0.113	0.035	0.998	16	9.9		28065

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)	Redundancy	Number Unique Reflections (All)
1	2.1	2.16			0.579	0.614	0.198	0.926		9.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (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 Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.097	39.443	28008	1384	99.46	0.197	0.1954	0.21	0.2362	0.25	0.05	25.821

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]
-3.088			2.935		0.153

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	16.069
r_dihedral_angle_6_deg	14.227
r_dihedral_angle_2_deg	6.302
r_lrange_it	5.829
r_lrange_other	5.739
r_dihedral_angle_1_deg	5.104
r_scangle_it	4.488
r_scangle_other	4.488
r_scbond_it	2.909
r_scbond_other	2.909
r_mcangle_it	2.671
r_mcangle_other	2.671
r_mcbond_it	1.812
r_mcbond_other	1.81
r_angle_refined_deg	1.356
r_angle_other_deg	0.444
r_nbd_refined	0.22
r_symmetry_nbd_refined	0.206
r_xyhbond_nbd_refined	0.197
r_nbd_other	0.186
r_nbtor_refined	0.18
r_symmetry_nbd_other	0.176
r_symmetry_xyhbond_nbd_refined	0.099
r_symmetry_nbtor_other	0.075
r_chiral_restr	0.064
r_metal_ion_refined	0.037
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3486
Nucleic Acid Atoms
Solvent Atoms	198
Heterogen Atoms	45

Software

Software
Software Name	Purpose
REFMAC	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing