4N18 | pdb_00004n18

Crystal structure of D-isomer specific 2-hydroxyacid dehydrogenase family protein from Klebsiella pneumoniae 342

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	289	0.2 ul of 15 mg/ml protein in 20mM HEPES pH 7.5, 150 mM NaCl, 10% Glycerol, 0.1% Sodium Azide and 0.5mM TCEP were mixed with 0.2 ul of The MCSG-I condition #88 (0.1M Sodium Citrate:HCL pH 5.6, 20% (v/v) 2-Propanol, 20% (w/v)PEG 4000) and equilibrated against 1.9 M NaCl in QIAGEN EasyXtal 15-Well Tool plate, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.567	α = 90
b = 76.567	β = 90
c = 101.281	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	ADSC QUANTUM 315	Rosenbaum-Rock vertical focusing mirror, with Pt, glass, Pd lanes	2013-06-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97912	APS	19-ID

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	1.97	50	99.6	0.075	0.075	44	10.9	22004	21916		-3	39.6

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	1.97	2	97.8		0.989	1.9	1.9	9.5	1050

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	SAD	THROUGHOUT	1.97	35.84	21950	21871	1124	99.64	0.1833	0.1812	0.19	0.2199	0.22	RANDOM	45.1758

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]
-1.35			-1.35		2.71

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.485
r_dihedral_angle_3_deg	16.273
r_dihedral_angle_4_deg	15.337
r_dihedral_angle_1_deg	6.178
r_angle_refined_deg	1.836
r_angle_other_deg	0.869
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	30.485
r_dihedral_angle_3_deg	16.273
r_dihedral_angle_4_deg	15.337
r_dihedral_angle_1_deg	6.178
r_angle_refined_deg	1.836
r_angle_other_deg	0.869
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.01
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2383
Nucleic Acid Atoms
Solvent Atoms	113
Heterogen Atoms	26

Software

Software
Software Name	Purpose
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-3000	data collection
HKL-3000	data reduction
HKL-3000	data scaling
HKL-3000	phasing
SHELXD	phasing
MLPHARE	phasing
SOLVE	phasing
RESOLVE	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.