4XA8 | pdb_00004xa8

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase from Xanthobacter autotrophicus Py2

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3KBO

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	0.2 UL OF 11 MG/ML PROTEIN IN 20 MM HEPES PH 7.5, 150 MM NACL, 10% GLYCEROL, 0.1% SODIUM AZIDE, 0.5 MM TCEP and 10 mM NADH WERE MIXED WITH 0.2 UL OF THE TOP96 CONDITION #34 (0.2M MAGNESIUM CHLORIDE, 6-HYDRATE, 0.1M HEPES, 25%W/V PEG 3350 PH=7.5) AND EQUILIBRATED AGAINST 1.5 M NACL SOLUTION IN 96 WELL 3 DROP CRYSTALLIZATION PLATE (SWISSCI). BEFORE CRYSTALLIZATION PROTEIN WAS INCUBATED WITH 1/50 V/V OF 1 MG/ML TEV SOLUTION AT 289 K FOR 1 HOUR

Crystal Properties
Matthews coefficient	Solvent content
1.95	41.13

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 58.762	α = 90
b = 63.714	β = 90
c = 154.967	γ = 90

Symmetry
Space Group	C 2 2 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	MARMOSAIC 300 mm CCD	Beryllium Lenses	2014-11-06	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.978	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	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	1.9	50	95.2	0.069	0.073	0.023	21.738	9		22335

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.93	96.9		0.835	0.881	0.276	0.786	2.6	9.6	1110

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 (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	3KBO	1.9	50	22262	1098	95.2	0.1655	0.1632	0.17	0.2086	0.22	RANDOM	39.663

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]
-0.82			-1.24		2.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.127
r_dihedral_angle_4_deg	16.421
r_dihedral_angle_3_deg	13.682
r_dihedral_angle_1_deg	5.555
r_mcangle_it	2.154
r_angle_refined_deg	1.639
r_mcbond_it	1.518
r_mcbond_other	1.518
r_angle_other_deg	0.837
r_chiral_restr	0.093
r_bond_refined_d	0.013
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2270
Nucleic Acid Atoms
Solvent Atoms	173
Heterogen Atoms

Software

Software
Software Name	Purpose
BLU-MAX	data collection
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing
HKL-3000	phasing
REFMAC	refinement
Coot	model building
PDB_EXTRACT	data extraction