8AM6 | pdb_00008am6

Cyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrificans K601 complexed with dehydrogenated substrate cyclohex-2-en-1-one - inactive mutant (Y195F)

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		289	240 mM ammonium citrate tribasic 20% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
2.67	53.96

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 66.03	α = 90
b = 121.7	β = 90
c = 158.15	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 EIGER2 X 16M		2019-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9763	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	Rrim 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	1.33	60.932	99.9	0.15	1	8.3	7.5		290848

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.33	1.35			0.6	1.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	8am3	1.33	60.932	290724	14422	99.863	0.175	0.175	0.174	0.17	0.1947	0.19	RANDOM	17.368

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.42
r_dihedral_angle_4_deg	19.573
r_dihedral_angle_3_deg	11.352
r_dihedral_angle_1_deg	6.683
r_lrange_it	5.251
r_scangle_it	3.649
r_scbond_it	2.617
r_angle_refined_deg	1.789
r_mcangle_it	1.781
r_mcbond_it	1.261
r_nbtor_refined	0.318
r_symmetry_nbd_refined	0.234
r_nbd_refined	0.223
r_xyhbond_nbd_refined	0.181
r_symmetry_xyhbond_nbd_refined	0.147
r_chiral_restr	0.117
r_ncsr_local_group_1	0.051
r_gen_planes_refined	0.014
r_bond_refined_d	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8264
Nucleic Acid Atoms
Solvent Atoms	1292
Heterogen Atoms	369

Software

Software
Software Name	Purpose
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing
SHELXDE	phasing
Coot	model building
CRANK	phasing