3B6B | pdb_00003b6b

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

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1B8Q	PDB ENTRY 1B8Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	40-45% MPD, 0.1M Hepes, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.839	α = 90
b = 152.528	β = 90
c = 184.12	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	ADSC QUANTUM 315	mirrors	2007-04-27	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A	0.98025	ESRF	BM30A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	76	98.6	0.06	0.06	7.3	4.7		72791			31.9

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2	2.11	98.7		0.303	0.303	2.6	4.8	10642

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	PDB ENTRY 1B8Q	2	20	70883	3757	98.28	0.20058	0.19907	0.2	0.22894	0.23	RANDOM	33.532

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		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.467
r_dihedral_angle_4_deg	20.477
r_dihedral_angle_3_deg	15.23
r_dihedral_angle_1_deg	5.999
r_scangle_it	2.836
r_scbond_it	1.673
r_angle_refined_deg	1.305
r_mcangle_it	1.223
r_mcbond_it	0.699
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.467
r_dihedral_angle_4_deg	20.477
r_dihedral_angle_3_deg	15.23
r_dihedral_angle_1_deg	5.999
r_scangle_it	2.836
r_scbond_it	1.673
r_angle_refined_deg	1.305
r_mcangle_it	1.223
r_mcbond_it	0.699
r_nbtor_refined	0.304
r_metal_ion_refined	0.221
r_symmetry_vdw_refined	0.213
r_nbd_refined	0.199
r_symmetry_hbond_refined	0.167
r_xyhbond_nbd_refined	0.131
r_chiral_restr	0.1
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6303
Nucleic Acid Atoms
Solvent Atoms	327
Heterogen Atoms	168

Software

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

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.