2PGN | pdb_00002pgn

The crystal structure of FAD and ThDP-dependent Cyclohexane-1,2-dione Hydrolase in Complex with Cyclohexane-1,2-dione

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	298	23% PEG 400, 0.01M sodium acetate, 3mM HEPES, 0.5mM ThDP, 0.5mM NAD, 0.1M NaCl. Crystal soaked in 47% PEG 400, 0.02M sodium acetate, 5mM 1,2 cyclohexanedione, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.18	43.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 123.6	α = 90
b = 123.6	β = 90
c = 144.3	γ = 90

Symmetry
Space Group	P 41 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	CCD	MARMOSAIC 225 mm CCD		2005-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.00	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	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	1.1	40	84.8	0.068	13.58	6.1	388867	379045			12.26

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.1	1.2	49.9		0.487	2.7	3.6	50802

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	known crystal structure	THROUGHOUT	1.2	10	333858	333858	16593	97.17	0.15	0.15	0.149	0.16	0.176	0.18	RANDOM	12.78

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]
0.75			0.75		-1.49

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.859
r_dihedral_angle_4_deg	16.822
r_dihedral_angle_3_deg	13.719
r_sphericity_free	8.377
r_dihedral_angle_1_deg	6.736
r_sphericity_bonded	5.477
r_scangle_it	4.005
r_scbond_it	3.235
r_mcangle_it	2.394
r_rigid_bond_restr	2.139
r_angle_refined_deg	2.052
r_mcbond_it	1.995
r_mcbond_other	1.766
r_angle_other_deg	1.391
r_symmetry_vdw_refined	0.317
r_symmetry_vdw_other	0.309
r_xyhbond_nbd_refined	0.25
r_nbd_refined	0.222
r_symmetry_hbond_refined	0.212
r_nbd_other	0.192
r_nbtor_refined	0.171
r_chiral_restr	0.128
r_nbtor_other	0.084
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8886
Nucleic Acid Atoms
Solvent Atoms	1268
Heterogen Atoms	290

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
XDS	data reduction