4RPF | pdb_00004rpf

Crystal structure of homoserine kinase from Yersinia pestis Nepal516, NYSGRC target 032715

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	294	PROTEIN IN 10 MM BIS-TRIS, 500 MM SODIUM CHLORIDE, 10% GLYCEROL, 5 MM DTT, 10 MM D-GLUCOSE, RESERVOIR: 0.17 M AMMONIUM ACETATE, 0.085 M SODIUM CITRATE, PH 5.6, 25.5% W/V PEG4000, 15% W/V GLYCEROL, 0.5 M 2-Aminoethylphosphonate; CRYOPROTECTANT = RESERVOIR, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 294K

Crystal Properties
Matthews coefficient	Solvent content
4.13	70.23

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 162.861	α = 90
b = 93.659	β = 90.14
c = 107.617	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	ADSC QUANTUM 315r	MIRRORS	2014-09-05	M	SINGLE WAVELENGTH

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

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	2.3	50	98.6	0.084	0.084	18.25	6		70518		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.34	97.9		1.5	6

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-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	NONE	2.3	40.72	68460	2024	97.36	0.24189	0.24038	0.2423	0.29054	0.2869	RANDOM	57.805

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]
-23.95		20.42	26.76		-2.81

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.186
r_scbond_other	23.071
r_scbond_it	23.065
r_long_range_B_refined	22.639
r_long_range_B_other	22.638
r_scangle_other	22.016
r_mcbond_other	19.483
r_mcbond_it	19.482
r_mcangle_it	18.682
r_mcangle_other	18.681
r_dihedral_angle_3_deg	15.186
r_dihedral_angle_4_deg	14.837
r_dihedral_angle_1_deg	5.277
r_angle_refined_deg	1.109
r_angle_other_deg	0.732
r_chiral_restr	0.063
r_bond_refined_d	0.006
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6982
Nucleic Acid Atoms
Solvent Atoms	93
Heterogen Atoms	39

Software

Software
Software Name	Purpose
SHELX	model building
BUCCANEER	model building
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
SHELX	phasing
BUCCANEER	phasing