5SI8 | pdb_00005si8

CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH c1(cn(nc1C(=O)Nc3cc2nc(cn2cc3C#N)c4ccccc4)C)C(=O)N5CCOCC5, micromolar IC50=0.060125

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
other		inhouse model

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	295	5-20 mg/mL protein in 25mM HEPES/NaOH pH7.5, 150mM NaCl, 50mM BME mixed 1:1 with reservoir 0.1M HEPES/NaOH pH7.5, 30% PEG550MME, 50mM MgCl2

Crystal Properties
Matthews coefficient	Solvent content
2.62	53

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.16	α = 90
b = 135.16	β = 90
c = 234.727	γ = 120

Symmetry
Space Group	H 3

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	MARMOSAIC 225 mm CCD		2009-07-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.999900	SLS	X10SA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim 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	2.1	41.51	73.6	0.065	0.079	0.998	9.65	2.123		69123			44.53

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.1	2.15	75		1.036	1.271	0.426	1.2	2.074

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	inhouse model	2.1	33.88	67524	3542	76.13	0.1981	0.1957	0.2014	0.2457	0.2501	RANDOM	42.518

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]
-0.21	-0.11		-0.21		0.7

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.954
r_dihedral_angle_4_deg	17.504
r_dihedral_angle_3_deg	15.035
r_dihedral_angle_1_deg	5.831
r_mcangle_it	3.526
r_mcbond_other	2.518
r_mcbond_it	2.517
r_angle_refined_deg	1.352
r_angle_other_deg	1.255
r_chiral_restr	0.065

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.954
r_dihedral_angle_4_deg	17.504
r_dihedral_angle_3_deg	15.035
r_dihedral_angle_1_deg	5.831
r_mcangle_it	3.526
r_mcbond_other	2.518
r_mcbond_it	2.517
r_angle_refined_deg	1.352
r_angle_other_deg	1.255
r_chiral_restr	0.065
r_bond_refined_d	0.006
r_gen_planes_refined	0.006
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10152
Nucleic Acid Atoms
Solvent Atoms	417
Heterogen Atoms	144

Software

Software
Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.