8AM8 | pdb_00008am8

Cyclohexanone dehydrogenase (CDH) from Alicycliphilus denitrificans K601 complexed with dehydrogenated substrate - W113A mutant

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 = 90.051	α = 90
b = 90.051	β = 90
c = 277.358	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 EIGER X 16M		2019-02-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.97625	Diamond	I04-1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	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	1.85	85.65	99.88	0.973	7	2.6		98195			20.861

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	1.85	1.88	99.2		0.999	1.3

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-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	1.85	85.65	98192	4802	99.878	0.175	0.1731	0.17	0.2154	0.22	RANDOM	25.769

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]
-0.002			-0.002		0.004

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.24
r_dihedral_angle_4_deg	19.599
r_dihedral_angle_3_deg	12.363
r_dihedral_angle_1_deg	6.902
r_lrange_it	4.858
r_scangle_it	4.003
r_scbond_it	2.791
r_mcangle_it	2.294
r_mcbond_it	1.682
r_angle_refined_deg	1.376
r_symmetry_nbd_refined	0.323
r_nbtor_refined	0.313
r_nbd_refined	0.211
r_symmetry_xyhbond_nbd_refined	0.134
r_xyhbond_nbd_refined	0.121
r_chiral_restr	0.099
r_ncsr_local_group_1	0.062
r_gen_planes_refined	0.008
r_bond_refined_d	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8173
Nucleic Acid Atoms
Solvent Atoms	657
Heterogen Atoms	197

Software

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