8AM3 | pdb_00008am3

Cyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrificans K601 - wildtype

X-RAY DIFFRACTION

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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
2.22	44.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.699	α = 90
b = 90.699	β = 90
c = 278.239	γ = 90

Symmetry
Space Group	P 43 21 2

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		2017-09-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	1.6	Diamond	I04-1

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	1.86	90.7	98.8	0.131	1	15.1	5.08		97297

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	1.86	1.89	83.1		0.4	0.9

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	SAD	THROUGHOUT	1.86	86.233	96606	4719	98.16	0.172	0.1705	0.17	0.2071	0.21	RANDOM	25.086

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]
0.001			0.001		-0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.644
r_dihedral_angle_4_deg	19.451
r_dihedral_angle_3_deg	11.806
r_dihedral_angle_1_deg	6.627
r_lrange_it	5.177
r_scangle_it	4.053
r_scbond_it	2.768
r_mcangle_it	2.382
r_mcbond_it	1.729
r_angle_refined_deg	1.427
r_nbtor_refined	0.313
r_symmetry_nbd_refined	0.266
r_nbd_refined	0.208
r_symmetry_xyhbond_nbd_refined	0.165
r_xyhbond_nbd_refined	0.139
r_chiral_restr	0.101
r_ncsr_local_group_1	0.065
r_gen_planes_refined	0.009
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8196
Nucleic Acid Atoms
Solvent Atoms	910
Heterogen Atoms	127

Software

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