1Q92

Crystal structure of human mitochondrial deoxyribonucleotidase in complex with the inhibitor PMcP-U

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.3	298	PEG 8000, potassium phosphate, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.63	52.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 73.758	α = 90
b = 73.758	β = 90
c = 105.981	γ = 90

Symmetry
Space Group	P 43 21 2

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	ADSC QUANTUM 4		2001-12-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-2	0.933	ESRF	ID14-2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.4	30				209551

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.4	1.45

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 1MH9	1.4	25.32	37528	35599	1929	64.83	0.13503	0.13337	0.16454	RANDOM	17.719

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]
0.16			0.16		-0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_1_deg	6.325
r_sphericity_free	5.48
r_scangle_it	4.797
r_sphericity_bonded	3.822
r_scbond_it	3.304
r_mcangle_it	2.586
r_rigid_bond_restr	1.947
r_angle_refined_deg	1.856
r_mcbond_it	1.73
r_angle_other_deg	1.008
r_nbd_refined	0.501
r_symmetry_vdw_other	0.385
r_symmetry_vdw_refined	0.301
r_symmetry_hbond_refined	0.29
r_nbd_other	0.252
r_xyhbond_nbd_refined	0.249
r_chiral_restr	0.132
r_nbtor_other	0.086
r_bond_refined_d	0.02
r_gen_planes_other	0.019
r_gen_planes_refined	0.014
r_bond_other_d	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1602
Nucleic Acid Atoms
Solvent Atoms	326
Heterogen Atoms	26

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing