2CJ9

Crystal structure of Methanosarcina barkeri seryl-tRNA synthetase complexed with an analog of seryladenylate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.9	294	PROTEIN WAS CRYSTALLIZED FROM 5-9% MPD, 50 MM MES, PH 5.9, 294 K, HANGING DROP VAPOR DIFFUSION

Crystal Properties
Matthews coefficient	Solvent content
3.14	60.49

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 96.713	α = 90
b = 96.713	β = 90
c = 270.302	γ = 120

Symmetry
Space Group	P 32 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	100	CCD	MARRESEARCH		2005-02-18	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06SA		SLS	X06SA

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	15	90.4	0.06	19.9	3.9		59591		2

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	2.3	2.38	94.9		0.24	4.1	3.9

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.3	14.93	49301	2567	78.8	0.208	0.206	0.248	RANDOM	72.35

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.591
r_dihedral_angle_3_deg	15.878
r_dihedral_angle_4_deg	15.678
r_dihedral_angle_1_deg	5.155
r_scangle_it	1.206
r_angle_refined_deg	1.066
r_scbond_it	0.745
r_mcangle_it	0.657
r_mcbond_it	0.382
r_nbtor_refined	0.298
r_nbd_refined	0.179
r_xyhbond_nbd_refined	0.177
r_symmetry_vdw_refined	0.114
r_chiral_restr	0.074
r_symmetry_hbond_refined	0.074
r_bond_refined_d	0.007
r_gen_planes_refined	0.003
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7899
Nucleic Acid Atoms
Solvent Atoms	330
Heterogen Atoms	62

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling