3L0S | pdb_00003l0s

Crystal structures of Zinc, Cobalt and Iron containing Adenylate kinase from Gram-negative bacteria Desulfovibrio gigas

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	277	0.2 M tartrate Na/K, 0.1 M MES (pH 6.5) and 20% PEG 2K, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 131.43	α = 90
b = 39.49	β = 109.31
c = 94.2	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 4		2007-06-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID29	1.6064	ESRF	ID29

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	R Sym I (Observed)	Rrim I (All)	Rpim I (All)	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	88.891	97.2	0.076	0.076	0.105	0.056	13.3	3.5	30472	30472

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Rrim I (All)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.11	94.6		0.426	0.426	0.61	0.32	1.7	3.5	4280

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	44.46	30458	1538	97.15	0.193	0.19	0.2	0.254	0.26	RANDOM	25.163

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]
-0.01		-0.02	0.03		-0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.994
r_dihedral_angle_4_deg	20.444
r_dihedral_angle_3_deg	16.778
r_dihedral_angle_1_deg	6.069
r_scangle_it	5.078
r_scbond_it	3.23
r_angle_refined_deg	1.902
r_mcangle_it	1.677
r_mcbond_it	0.985
r_chiral_restr	0.141

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.994
r_dihedral_angle_4_deg	20.444
r_dihedral_angle_3_deg	16.778
r_dihedral_angle_1_deg	6.069
r_scangle_it	5.078
r_scbond_it	3.23
r_angle_refined_deg	1.902
r_mcangle_it	1.677
r_mcbond_it	0.985
r_chiral_restr	0.141
r_bond_refined_d	0.021
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3397
Nucleic Acid Atoms
Solvent Atoms	302
Heterogen Atoms	22

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing
DM	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection

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.