6CSW

Crystal Structure of the Human vaccinia-related kinase bound to a N-methyl-N-propyl-dihydropteridine inhibitor

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3OP5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	293	27.5% PEG3350; 300 mM LiSO4; 0.1M SBG pH 7.0

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.83	α = 90
b = 96.987	β = 90
c = 191.67	γ = 90

Symmetry
Space Group	P 21 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 PILATUS3 6M		2017-12-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I24	0.96861	Diamond	I24

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	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	2.25	34.8	100	0.192	0.226	0.119	0.993	8.3	6.7		81966

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	Rpim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.29	99.9		1.108	1.321	0.711	0.683	1.7	6.5

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	3OP5	2.25	34.8	77901	3987	99.95	0.18977	0.18757	0.23289	RANDOM	35.987

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]
-0.39			1.78		-1.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.946
r_dihedral_angle_4_deg	15.12
r_dihedral_angle_3_deg	13.937
r_dihedral_angle_1_deg	6.051
r_long_range_B_refined	4.739
r_long_range_B_other	4.738
r_angle_refined_deg	1.231
r_mcangle_it	1.116
r_mcangle_other	1.116
r_scangle_other	0.948
r_angle_other_deg	0.775
r_mcbond_it	0.605
r_mcbond_other	0.605
r_scbond_it	0.597
r_scbond_other	0.597
r_chiral_restr	0.071
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
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	9905
Nucleic Acid Atoms
Solvent Atoms	534
Heterogen Atoms	250

Software

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