2O8H | pdb_00002o8h

Crystal structure of the catalytic domain of rat phosphodiesterase 10A

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
in silico model	Other		homology model of PDE10a

Crystallization

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.42

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.622	α = 90
b = 120.622	β = 90
c = 82.143	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	IMAGE PLATE	RIGAKU RAXIS IIC	mirrors	2002-05-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RU200	1.5418

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	1.8	30	91.4	0.063	12.2			37865

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)
	1.8	1.86	53.9		0.675			2236

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	homology model of PDE10a	1.8	30	37822	2905	91.58	0.227	0.224	0.23	0.273	0.28	RANDOM	35.117

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]
-2.27	-1.13		-2.27		3.4

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	5.391
r_scangle_it	3.245
r_scbond_it	2.071
r_angle_refined_deg	1.476
r_mcangle_it	1.312
r_angle_other_deg	0.896
r_mcbond_it	0.742
r_symmetry_hbond_refined	0.254
r_nbd_other	0.245
r_xyhbond_nbd_refined	0.233
r_nbd_refined	0.231
r_symmetry_vdw_other	0.21
r_metal_ion_refined	0.162
r_symmetry_vdw_refined	0.129
r_nbtor_other	0.086
r_chiral_restr	0.085
r_bond_refined_d	0.017
r_gen_planes_refined	0.006
r_gen_planes_other	0.003
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2491
Nucleic Acid Atoms
Solvent Atoms	312
Heterogen Atoms	36

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data reduction