2RIR

Crystal structure of dipicolinate synthase, A chain, from Bacillus subtilis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	294	0.2 M Lithium sulfate, 0.1 M Tris buffer, 25% PEG 3350, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
3.29	62.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 261.578	α = 90
b = 75.108	β = 119.74
c = 200.464	γ = 90

Symmetry
Space Group	C 1 2 1

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	SBC-2		2003-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID	0.97920	APS	19-ID

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	2.79	40	97	0.146	5.5		81355	81355			61.3

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	2.79	2.9	88.6		0.774	1.37		7396

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION		THROUGHOUT	2.79	40	81346	81346	4079	96.38	0.2011	0.2011	0.1986	0.2494	RANDOM	35.904

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]
0.7		-1.27	-1.19		-0.77

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.811
r_dihedral_angle_3_deg	23.213
r_dihedral_angle_4_deg	22.557
r_dihedral_angle_1_deg	5.954
r_scangle_it	2.223
r_angle_refined_deg	1.57
r_scbond_it	1.333
r_mcangle_it	0.939
r_mcbond_it	0.565
r_nbtor_refined	0.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.811
r_dihedral_angle_3_deg	23.213
r_dihedral_angle_4_deg	22.557
r_dihedral_angle_1_deg	5.954
r_scangle_it	2.223
r_angle_refined_deg	1.57
r_scbond_it	1.333
r_mcangle_it	0.939
r_mcbond_it	0.565
r_nbtor_refined	0.32
r_symmetry_vdw_refined	0.266
r_nbd_refined	0.244
r_symmetry_hbond_refined	0.189
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.11
r_bond_refined_d	0.013
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	17942
Nucleic Acid Atoms
Solvent Atoms	121
Heterogen Atoms	391

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
SBC-Collect	data collection
HKL-2000	data reduction
SHELXD	phasing
SOLVE	phasing
RESOLVE	phasing
HKL-2000	data scaling

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.