1YXD | pdb_00001yxd

Structure of E. coli dihydrodipicolinate synthase bound with allosteric inhibitor (S)-lysine to 2.0 A

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	10	276	1.8M potassium phosphate, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 276K

Crystal Properties
Matthews coefficient	Solvent content
3.72	66.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 121.148	α = 90
b = 121.148	β = 90
c = 110.084	γ = 120

Symmetry
Space Group	P 31 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		IMAGE PLATE	RIGAKU RAXIS IV		2004-09-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	37.99	100	0.088	14.9	10.88		63306	2	2

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	2.07	100		0.356	6.1	6.1

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2	37.99	60077	3225	100	0.16074	0.15933	0.17	0.18611	0.18	RANDOM	19.854

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]
-0.18	-0.09		-0.18		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.849
r_dihedral_angle_4_deg	17.089
r_dihedral_angle_3_deg	15.372
r_dihedral_angle_1_deg	6.125
r_scangle_it	3.779
r_scbond_it	2.357
r_angle_refined_deg	1.531
r_mcangle_it	1.307
r_angle_other_deg	0.901
r_mcbond_it	0.7
r_symmetry_hbond_refined	0.272
r_symmetry_vdw_other	0.252
r_nbd_refined	0.233
r_nbd_other	0.186
r_mcbond_other	0.179
r_symmetry_vdw_refined	0.173
r_nbtor_refined	0.168
r_metal_ion_refined	0.163
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.101
r_nbtor_other	0.092
r_bond_refined_d	0.014
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4321
Nucleic Acid Atoms
Solvent Atoms	557
Heterogen Atoms	34

Software

Software
Software Name	Purpose
REFMAC	refinement
d*TREK	data scaling
AMoRE	phasing