3D0C | pdb_00003d0c

Crystal structure of dihydrodipicolinate synthase from Oceanobacillus iheyensis at 1.9 A resolution

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	293	0.2M Magnesium chloride, 0.1M Lysine, 3% DMSO, 0.1M Tris-HCl pH 8.5, 25% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.28	45.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.037	α = 90
b = 57.063	β = 90
c = 71.457	γ = 90

Symmetry
Space Group	P 21 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	Mirrors	2008-04-21	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.97920	NSLS	X29A

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	1.9	50	96.1	0.074	10.4	11.3	50112	50112			17.5

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)
	1.9	1.97	85		0.35		8.2	4270

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	SAD	THROUGHOUT	1.9	50	50112	48326	1946	93.9	0.235	0.218	0.218	0.2169	0.243	0.242	RANDOM	27.4

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]
-7.56			5.25		2.31

RMS Deviations
Key	Refinement Restraint Deviation
C_dihedral_angle_deg	20.7
c_angle_deg	1.2
C_improper_angle_deg	0.8
c_angle_d	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4705
Nucleic Acid Atoms
Solvent Atoms	442
Heterogen Atoms

Software

Software
Software Name	Purpose
CBASS	data collection
SHELXCD	phasing
SHARP	phasing
CNS	refinement
DENZO	data reduction
HKL-2000	data scaling