3CKY | pdb_00003cky

Structural and Kinetic Properties of a beta-hydroxyacid dehydrogenase involved in nicotinate fermentation

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	5.5	291	19% PEG 8000, 0.1 M Sodium cacodylate, 0.1 M Ammonium sulfate, pH 5.5, VAPOR DIFFUSION, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.47	50.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.978	α = 90
b = 175.779	β = 90
c = 83.709	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	CCD	MARRESEARCH		2005-09-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.9795	EMBL/DESY, HAMBURG	BW7A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym 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	2.3	41.849	94.1	0.109	0.109	5.2	4.6		55151

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.42	77.2		0.384	0.384	2	3.7	6091

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 (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	2.3	24.47	55151	52485	2674	95.06	0.195	0.194	0.2033	0.222	0.2335	RANDOM	43.011

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]
-3.08			1.55		1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	39.361
r_dihedral_angle_4_deg	15.398
r_dihedral_angle_3_deg	15.286
r_dihedral_angle_1_deg	5.376
r_scangle_it	1.878
r_scbond_it	1.279
r_angle_refined_deg	1.063
r_angle_other_deg	0.871
r_mcbond_it	0.548
r_mcangle_it	0.548
r_symmetry_vdw_other	0.227
r_nbd_refined	0.203
r_symmetry_hbond_refined	0.197
r_symmetry_vdw_refined	0.179
r_nbd_other	0.175
r_nbtor_refined	0.165
r_xyhbond_nbd_refined	0.159
r_nbtor_other	0.086
r_mcbond_other	0.085
r_chiral_restr	0.057
r_xyhbond_nbd_other	0.045
r_bond_refined_d	0.009
r_gen_planes_refined	0.003
r_gen_planes_other	0.002
r_bond_other_d	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8045
Nucleic Acid Atoms
Solvent Atoms	447
Heterogen Atoms

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MOSFLM	data reduction