9FL6 | pdb_00009fl6

Human NUDT1 with medetomidine

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		NUDT1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP		277	30% PEG8000, 0.2 M lithium sulfate and 0.1 M acetate pH 4.5

Crystal Properties
Matthews coefficient	Solvent content
2.09	41.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.739	α = 90
b = 60.85	β = 90
c = 67.53	γ = 90

Symmetry
Space Group	P 2 21 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	PIXEL	DECTRIS PILATUS 2M		2015-07-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I04-1	0.928190	Diamond	I04-1

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	1.3	67.53	99.9	0.061	13.4	6.5		38033

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	1.3	1.32	99.9		0.693		5.4

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	1.3	45.205	37960	1935	99.868	0.161	0.1592	0.1674	0.2065	0.2062	16.151

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]
0.413			-0.492		0.078

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.714
r_dihedral_angle_4_deg	11.251
r_dihedral_angle_3_deg	10.718
r_dihedral_angle_1_deg	7.315
r_lrange_it	2.968
r_lrange_other	2.967
r_scangle_it	2.184
r_scangle_other	2.184
r_mcangle_other	1.755
r_mcangle_it	1.751
r_scbond_it	1.683
r_scbond_other	1.682
r_angle_refined_deg	1.428
r_angle_other_deg	1.311
r_mcbond_it	1.254
r_mcbond_other	1.241
r_rigid_bond_restr	1.118
r_symmetry_nbd_refined	0.286
r_nbd_refined	0.202
r_symmetry_nbd_other	0.172
r_nbtor_refined	0.163
r_nbd_other	0.144
r_xyhbond_nbd_refined	0.117
r_symmetry_xyhbond_nbd_refined	0.116
r_chiral_restr	0.077
r_symmetry_nbtor_other	0.072
r_gen_planes_refined	0.007
r_bond_refined_d	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	1246
Nucleic Acid Atoms
Solvent Atoms	132
Heterogen Atoms	19

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
PHASER	phasing