2YXG | pdb_00002yxg

Crystal structure of Dihyrodipicolinate Synthase (dapA)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1O5K

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	Oil-batch	6.5	293	18% PEG 8000, 0.1M Cacodylate, 0.2M Ca Acetate, pH 6.5, Oil-batch, temperature 293.0K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.469	α = 90
b = 76.532	β = 106.87
c = 101.863	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	120	CCD	MARMOSAIC 225 mm CCD			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SRS BEAMLINE PX10.1	0.979	SRS	PX10.1

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	2.2	50	97.6	0.067		3.9	59985	58517	-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)
	2.2	2.28	82.6		0.211		2.7	4918

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-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1O5K	2.2	20	55463	2965	97.47	0.16115	0.15774	0.22444	RANDOM	26.881

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]
-1.97		-0.9	0.98		0.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.514
r_dihedral_angle_4_deg	19.352
r_dihedral_angle_3_deg	16.061
r_dihedral_angle_1_deg	6.852
r_scangle_it	5.369
r_scbond_it	3.374
r_angle_refined_deg	1.825
r_mcangle_it	1.721
r_mcbond_it	1.164
r_nbtor_refined	0.311

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.514
r_dihedral_angle_4_deg	19.352
r_dihedral_angle_3_deg	16.061
r_dihedral_angle_1_deg	6.852
r_scangle_it	5.369
r_scbond_it	3.374
r_angle_refined_deg	1.825
r_mcangle_it	1.721
r_mcbond_it	1.164
r_nbtor_refined	0.311
r_nbd_refined	0.246
r_symmetry_vdw_refined	0.229
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.129
r_symmetry_hbond_refined	0.128
r_bond_refined_d	0.022
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8849
Nucleic Acid Atoms
Solvent Atoms	700
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
HKL-2000	data reduction
SCALEPACK	data scaling
MOLREP	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.