8S00 | pdb_00008s00

CpKRS complexed with lysine and an inhibitor

X-RAY DIFFRACTION

---

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		internal model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	Protein buffer: 25 mM HEPES, 500 mM NaCl, 5% glycerol, 0.5 mM TCEP, pH 7, 30 mg/ml Reservoir: 0.2 M Li2SO4, 14-18% PEG3350, 0.1 M tris pH 7.4-7.8

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.987	α = 90
b = 121.761	β = 90
c = 143.092	γ = 90

Symmetry
Space Group	P 2 21 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER2 XE 16M		2020-10-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.97627	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	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	56.08	100	0.223	0.09	0.997	8.7	13.8		86869			27.96

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.04	100		2.516	1.002	0.494	1.2	14.1

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2	56.08	86793	4333	99.976	0.184	0.1822	0.1899	0.2218	0.2279	33.068

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]
-1.827			2.749		-0.923

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_6_deg	14.504
r_dihedral_angle_3_deg	12.578
r_dihedral_angle_2_deg	8.052
r_dihedral_angle_1_deg	6.922
r_lrange_it	6.34
r_lrange_other	6.3
r_scangle_it	5.301
r_scangle_other	5.301
r_scbond_it	3.514
r_scbond_other	3.514
r_mcangle_it	3.453
r_mcangle_other	3.452
r_mcbond_it	2.55
r_mcbond_other	2.549
r_angle_refined_deg	1.458
r_angle_other_deg	0.517
r_nbd_other	0.212
r_nbd_refined	0.208
r_symmetry_nbd_other	0.189
r_symmetry_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.18
r_symmetry_nbd_refined	0.172
r_xyhbond_nbd_refined	0.163
r_symmetry_nbtor_other	0.079
r_chiral_restr	0.073
r_ncsr_local_group_1	0.062
r_gen_planes_refined	0.007
r_bond_refined_d	0.006
r_symmetry_xyhbond_nbd_other	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8098
Nucleic Acid Atoms
Solvent Atoms	696
Heterogen Atoms	112

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data reduction
Aimless	data scaling
PHASER	phasing