2OLC | pdb_00002olc

Crystal structure of 5-methylthioribose kinase in complex with ADP-2Ho

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	298	22%(w/v) PEG2000MME, 0.1M TrisHCl pH 7.5 and 0.3M sodium acetate, vapor diffusion, hanging drop, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.57	52.14

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 215.2	α = 90
b = 83.6	β = 90
c = 51.6	γ = 90

Symmetry
Space Group	P 21 21 2

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 4r	mirrors	2003-08-27	M	SINGLE WAVELENGTH
2	1	x-ray	100	IMAGE PLATE	RIGAKU RAXIS IV++	osmic	2004-09-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	1.5362	NSLS	X8C
2	ROTATING ANODE	RIGAKU	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	71.73	98.8	0.093	21.9	26.94		63253		5

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	2.07	97.5		0.434	9.2	26.57	6169

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	SAD	THROUGHOUT	2	107.83	63173	3148	98.79	0.215	0.214	0.21	0.25	0.25	RANDOM	27.565

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]
-1.53			-0.23		1.76

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.241
r_dihedral_angle_4_deg	15.694
r_dihedral_angle_3_deg	14.56
r_dihedral_angle_1_deg	5.723
r_scangle_it	2.27
r_scbond_it	1.558
r_angle_refined_deg	1.324
r_mcangle_it	0.841
r_mcbond_it	0.495
r_nbtor_refined	0.305
r_symmetry_hbond_refined	0.258
r_symmetry_vdw_refined	0.204
r_nbd_refined	0.196
r_metal_ion_refined	0.165
r_xyhbond_nbd_refined	0.159
r_chiral_restr	0.085
r_bond_refined_d	0.01
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5917
Nucleic Acid Atoms
Solvent Atoms	434
Heterogen Atoms	87

Software

Software
Software Name	Purpose
d*TREK	data scaling
SHELX	phasing
RESOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction
SHELXDE	phasing