5SDV | pdb_00005sdv

CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 10 IN COMPLEX WITH c2(c(C(=O)NCc1cocn1)cnn2C)C(=O)Nc4nc3nc(cn3cc4)c5ccccc5, micromolar IC50=0.001258

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
2.63	53.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 135.343	α = 90
b = 135.343	β = 90
c = 235.651	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	PIXEL	PSI PILATUS 6M		2010-08-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.000000	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	2.15	43.73	99.9	0.114	0.127	0.998	11.62	5.239		87514			42.128

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	2.15	2.21	100		1.161	1.287	0.526	1.5	5.386

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	2.15	43.73	80331	4205	96.54	0.1779	0.1752	0.1833	0.2318	0.237	RANDOM	36.574

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]
-0.07	-0.04		-0.07		0.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.654
r_dihedral_angle_4_deg	20.363
r_dihedral_angle_3_deg	17.344
r_dihedral_angle_1_deg	6.399
r_mcangle_it	5.383
r_mcbond_it	4.246
r_mcbond_other	4.236
r_angle_refined_deg	2.146
r_angle_other_deg	1.521
r_chiral_restr	0.105

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.654
r_dihedral_angle_4_deg	20.363
r_dihedral_angle_3_deg	17.344
r_dihedral_angle_1_deg	6.399
r_mcangle_it	5.383
r_mcbond_it	4.246
r_mcbond_other	4.236
r_angle_refined_deg	2.146
r_angle_other_deg	1.521
r_chiral_restr	0.105
r_bond_refined_d	0.016
r_gen_planes_refined	0.013
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10140
Nucleic Acid Atoms
Solvent Atoms	582
Heterogen Atoms	140

Software

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