2X7G

Structure of human serine-arginine-rich protein-specific kinase 2 (SRPK2) bound to purvalanol B

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WBP	PDB ENTRY 1WBP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		4.75		0.5M AMMONIUM SULPHATE, 0.1M SODIUM ACETATE PH4.75

Crystal Properties
Matthews coefficient	Solvent content
3.6	65.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.31	α = 90
b = 110.31	β = 90
c = 90.59	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	100	CCD	RAYONIX		2009-09-28	M	SINGLE WAVELENGTH

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

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	2.5	45.21	99.7	0.13	6.5	3.2		22306			43.1

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	2.5	2.64	99.6		0.59	2	3.2

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	PDB ENTRY 1WBP	2.5	45	21171	1135	99.46	0.18615	0.18292	0.24868	RANDOM	16.352

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]
0.08	0.04		0.08		-0.12

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.143
r_dihedral_angle_4_deg	16.742
r_dihedral_angle_3_deg	14.205
r_scangle_it	9.999
r_scbond_it	7.692
r_dihedral_angle_1_deg	5.792
r_mcangle_it	4.091
r_mcbond_it	2.452
r_angle_refined_deg	1.368
r_angle_other_deg	0.865
r_mcbond_other	0.627
r_symmetry_vdw_other	0.262
r_nbd_refined	0.214
r_nbtor_refined	0.184
r_symmetry_hbond_refined	0.178
r_nbd_other	0.176
r_xyhbond_nbd_refined	0.137
r_symmetry_vdw_refined	0.099
r_nbtor_other	0.085
r_chiral_restr	0.076
r_bond_refined_d	0.013
r_gen_planes_refined	0.006
r_gen_planes_other	0.004
r_bond_other_d	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2765
Nucleic Acid Atoms
Solvent Atoms	111
Heterogen Atoms	93

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing