9R1Y | pdb_00009r1y

PLK1 SURFACE ENTROPY REDUCTION (SER) MUTANT IN COMPLEX WITH INHIBITOR GSK461364

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2V5Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	293	sodium acetate, ammonium sulphate, MES

Crystal Properties
Matthews coefficient	Solvent content
2.61	52.92

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.772	α = 90
b = 104.174	β = 115.309
c = 71.286	γ = 90

Symmetry
Space Group	C 1 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	MAR CCD 165 mm		2008-02-13	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	BESSY BEAMLINE 14.2	0.91841	BESSY	14.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.6	42.43	88.9	0.07	14.9	4.1		84640			45.3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.6	2.68			0.23	4.1

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	2.602	42.428	20518	1031	88.592	0.187	0.185	0.1878	0.2178	0.2149	68.082

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]
0.871		2.433	-2.466		-0.488

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.981
r_dihedral_angle_3_deg	13.358
r_dihedral_angle_4_deg	12.448
r_lrange_it	7.03
r_lrange_other	7.029
r_dihedral_angle_1_deg	5.513
r_scangle_it	4.821
r_scangle_other	4.82
r_mcangle_it	3.76
r_mcangle_other	3.759
r_scbond_it	2.934
r_scbond_other	2.933
r_mcbond_it	2.311
r_mcbond_other	2.31
r_angle_refined_deg	1.256
r_angle_other_deg	1.03
r_nbd_other	0.181
r_nbd_refined	0.17
r_symmetry_nbd_other	0.159
r_nbtor_refined	0.151
r_symmetry_nbd_refined	0.143
r_symmetry_xyhbond_nbd_refined	0.121
r_xyhbond_nbd_refined	0.099
r_symmetry_nbtor_other	0.069
r_ncsr_local_group_1	0.064
r_chiral_restr	0.042
r_chiral_restr_other	0.032
r_bond_refined_d	0.004
r_gen_planes_refined	0.002
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4735
Nucleic Acid Atoms
Solvent Atoms	56
Heterogen Atoms	147

Software

Software
Software Name	Purpose
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing