3EE3 | pdb_00003ee3

Crystal structure of Acanthamoeba polyphaga mimivirus nucleoside diphosphate kinase complexed with CDP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.4	293	40 to 44% MPD, 0.1M MOPS, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.04	59.57

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.419	α = 90
b = 154.419	β = 90
c = 187.039	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	2007-07-24	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	2.4	95.3	99.7	0.077	6	4.7	45481	45481			56.3

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)
	2.4	2.53	99.9		0.433	1.7	4.8	6609

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 (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	2.4	20	44357	2366	99.59	0.19635	0.1944	0.1951	0.23347	0.2347	RANDOM	47.789

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]
0.08			-0.12		0.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.851
r_dihedral_angle_4_deg	25.698
r_dihedral_angle_3_deg	17.887
r_dihedral_angle_1_deg	6.761
r_scangle_it	3.018
r_scbond_it	1.857
r_angle_refined_deg	1.542
r_mcangle_it	1.309
r_mcbond_it	0.732
r_nbtor_refined	0.299

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.851
r_dihedral_angle_4_deg	25.698
r_dihedral_angle_3_deg	17.887
r_dihedral_angle_1_deg	6.761
r_scangle_it	3.018
r_scbond_it	1.857
r_angle_refined_deg	1.542
r_mcangle_it	1.309
r_mcbond_it	0.732
r_nbtor_refined	0.299
r_symmetry_vdw_refined	0.222
r_nbd_refined	0.208
r_symmetry_hbond_refined	0.177
r_xyhbond_nbd_refined	0.147
r_chiral_restr	0.1
r_metal_ion_refined	0.078
r_bond_refined_d	0.015
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6312
Nucleic Acid Atoms
Solvent Atoms	157
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 R01GM157729.