7CWA | pdb_00007cwa

Crystal structure of PDE8A catalytic domain in complex with clofarabine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3ECN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		277	100 mM Cacodylate Sodium pH 6.5, 15% Isopropanol, 30% ethylene glycol, 11% PEG 3350

Crystal Properties
Matthews coefficient	Solvent content
3.38	63.62

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 76.261	α = 90
b = 132.246	β = 90
c = 101.916	γ = 90

Symmetry
Space Group	C 2 2 21

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	OXFORD ONYX CCD		2020-07-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SEALED TUBE	OXFORD DIFFRACTION NOVA	1.5406

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	2.8	24.26	99.7	0.096	15.84	4.6		13022

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	2.8	2.9	100		0.276	4.12

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	3ECN	2.8	24.26	11260	571	90.35	0.2909	0.28872	0.29	0.33298	0.33	RANDOM	37.493

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]
-2.95			-1.95		4.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.815
r_dihedral_angle_3_deg	11.823
r_dihedral_angle_4_deg	9.552
r_dihedral_angle_1_deg	4.69
r_long_range_B_refined	2.593
r_long_range_B_other	2.537
r_mcangle_it	0.971
r_mcangle_other	0.971
r_angle_refined_deg	0.914
r_angle_other_deg	0.849
r_mcbond_it	0.516
r_mcbond_other	0.516
r_scangle_other	0.47
r_scbond_it	0.215
r_scbond_other	0.215
r_chiral_restr	0.047
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2721
Nucleic Acid Atoms
Solvent Atoms	44
Heterogen Atoms	22

Software

Software
Software Name	Purpose
REFMAC	refinement
CrysalisPro	data reduction
CrysalisPro	data scaling
MOLREP	phasing