3EIC

X-ray structure of Acanthamoeba ployphaga mimivirus nucleoside diphosphate kinase complexed with UDP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	273	MPD 40 to 44%, MOPS 0.1M, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 273K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.472	α = 90
b = 152.726	β = 90
c = 184.94	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	110	CCD	ADSC QUANTUM 315	mirrors	2007-07-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.064	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	2.3	92.4	99.7	0.071	6	5		49557			47.885

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.3	2.42	100		0.331	2.3	5.1	7285

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	2b8q	2.3	20	48109	48109	2570	99.62	0.18997	0.18814	0.22437	RANDOM	42.298

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]
-0.03					0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.054
r_dihedral_angle_4_deg	24.046
r_dihedral_angle_3_deg	17.528
r_dihedral_angle_1_deg	6.398
r_scangle_it	3.293
r_scbond_it	1.965
r_angle_refined_deg	1.396
r_mcangle_it	1.315
r_mcbond_it	0.723
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.054
r_dihedral_angle_4_deg	24.046
r_dihedral_angle_3_deg	17.528
r_dihedral_angle_1_deg	6.398
r_scangle_it	3.293
r_scbond_it	1.965
r_angle_refined_deg	1.396
r_mcangle_it	1.315
r_mcbond_it	0.723
r_nbtor_refined	0.304
r_nbd_refined	0.213
r_symmetry_vdw_refined	0.208
r_xyhbond_nbd_refined	0.145
r_chiral_restr	0.096
r_symmetry_hbond_refined	0.08
r_bond_refined_d	0.012
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6338
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	156

Software

Software
Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

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 R01GM133198.