1WBP | pdb_00001wbp

SRPK1 bound to 9mer docking motif peptide

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		100MM SODIUM CITRATE PH5.6, 200MM AMMONIUM ACETATE, 15%PEG3350, 5MM PEPTIDE, 5MM ADP, 10MM MGCL2, pH 7.00

Crystal Properties
Matthews coefficient	Solvent content
2.99	58.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.68	α = 90
b = 78.68	β = 90
c = 310.54	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	105	CCD	ADSC CCD		2003-11-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 19-ID		APS	19-ID

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	2.4	30	97.8	0.07	8.1	11		22765		1	10.9

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	2.4	2.49	84		0.56	2.9	7.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1WAK	2.4	28.26	2	15613	476	67.1	0.228	0.228	0.247	RANDOM	96.2

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]
21.3	14.59		21.3		-42.61

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	21.2
c_mcangle_it	11.44
c_scangle_it	10.7
c_mcbond_it	8.48
c_scbond_it	8.26
c_angle_deg	1.4
c_improper_angle_d	0.74
c_bond_d	0.008
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2910
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	31

Software

Software
Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling
AMoRE	phasing