4G89 | pdb_00004g89

Crystal structure of k. pneumoniae mta/adohcy nucleosidase in complex with fragmented s-adenosyl-l-homocysteine

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		S.AUREUS MTAN

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	294	1.67M AMMONIUM SULPHATE, 80MM HEPES PH 7.5, 1.7% PEG 400, VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 115.346	α = 90
b = 59.242	β = 128.46
c = 82.926	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	110	IMAGE PLATE	RIGAKU RAXIS IV++	CAPILLIARY	2006-09-03	M	SINGLE WAVELENGTH
2	1	x-ray

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5418

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
1,2	2.1	30.64	100	0.097	13.6	3.9	25670	25670			24.34

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)
1,2	2.1	2.21	100		0.449	2.8	3.9	1671

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 (All)	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	S.AUREUS MTAN	2.1	30.64	25670	24376	1294	99.69	0.16307	0.16307	0.16005	0.17	0.21982	0.23	RANDOM	39.615

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]
4.7		2.89	-1.86		0.75

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.569
r_dihedral_angle_4_deg	21.974
r_dihedral_angle_3_deg	17.567
r_dihedral_angle_1_deg	13.554
r_angle_refined_deg	1.789
r_angle_other_deg	1.088
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.569
r_dihedral_angle_4_deg	21.974
r_dihedral_angle_3_deg	17.567
r_dihedral_angle_1_deg	13.554
r_angle_refined_deg	1.789
r_angle_other_deg	1.088
r_chiral_restr	0.106
r_bond_refined_d	0.016
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3450
Nucleic Acid Atoms
Solvent Atoms	278
Heterogen Atoms	31

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	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.