5MXX

Crystal structure of human SR protein kinase 1 (SRPK1) in complex with compound 1

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WAK	1wak, 1wbp
experimental model	PDB	1WBP	1wak, 1wbp

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	277.15	0.1 M tris pH 7.5, 0.1 M CaCl2, 20% PEG6K, 11% ethylene glycol

Crystal Properties
Matthews coefficient	Solvent content
2.51	51.11

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.572	α = 90
b = 82.572	β = 90
c = 133.837	γ = 90

Symmetry
Space Group	P 43 21 2

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 PILATUS 6M		2014-04-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I03	0.9795	Diamond	I03

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	1.75	29.29	99.8	0.059	0.023	28.4	14.2		47639			21.5

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.75	1.78	96		0.826	0.323	3.7	13.8

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	1wak, 1wbp	1.75	29.29	45207	2354	99.76	0.17479	0.1732	0.20533	RANDOM	29.591

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			-0.18		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.311
r_dihedral_angle_4_deg	16.44
r_dihedral_angle_3_deg	12.691
r_long_range_B_refined	6.357
r_long_range_B_other	6.263
r_dihedral_angle_1_deg	5.976
r_scangle_other	4.665
r_scbond_it	2.927
r_scbond_other	2.927
r_mcangle_other	2.787
r_mcangle_it	2.784
r_mcbond_it	1.913
r_mcbond_other	1.909
r_angle_refined_deg	1.546
r_angle_other_deg	0.951
r_chiral_restr	0.099
r_bond_refined_d	0.012
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.002
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	2932
Nucleic Acid Atoms
Solvent Atoms	216
Heterogen Atoms	86

Software

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