2HNK | pdb_00002hnk

Crystal structure of SAM-dependent O-methyltransferase from pathogenic bacterium Leptospira interrogans

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.3	277	0.1M lithium sulfate monohydrate, 0.1M MES pH 6.5, 9% w/v polyethylene glycol 8000, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
4.08	69.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 157.81	α = 90
b = 60.331	β = 90
c = 138.232	γ = 90

Symmetry
Space Group	P 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	IMAGE PLATE	RIGAKU RAXIS IV		2005-04-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	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	2.3	50	98.6	0.075	11	5	59471	58638

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)
	2.3	2.38	99.7		0.394		4.9	5833

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	2.3	30	59511	57726	2916	97	0.214	0.213	0.2093	0.243	0.2394	RANDOM	31.179

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]
-2.15			-0.78		2.93

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.224
r_dihedral_angle_4_deg	20.154
r_dihedral_angle_3_deg	15.465
r_dihedral_angle_1_deg	5.701
r_scangle_it	1.918
r_angle_refined_deg	1.173
r_scbond_it	1.17
r_mcangle_it	0.9
r_mcbond_it	0.511
r_nbtor_refined	0.303
r_xyhbond_nbd_refined	0.248
r_nbd_refined	0.188
r_symmetry_vdw_refined	0.159
r_symmetry_hbond_refined	0.119
r_chiral_restr	0.076
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5438
Nucleic Acid Atoms
Solvent Atoms	446
Heterogen Atoms	98

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
PHASER	phasing