2ODR | pdb_00002odr

Methanococcus Maripaludis Phosphoseryl-tRNA synthetase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	298	Well:4-6% PEG 35,000, 5 mM DTT, 100 mM Sodium MES (pH 6.5), 5% glycerol, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.9	57.54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 119.172	α = 90
b = 133.943	β = 90
c = 208.382	γ = 90

Symmetry
Space Group	P 21 21 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	CCD	ADSC QUANTUM 210			M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 315			M	MAD
3	1	x-ray	100	CCD	ADSC QUANTUM 210			M	SINGLE WAVELENGTH
1,2,3	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.00390	ALS	8.2.2
2	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.214	ALS	8.2.2
3	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0716	ALS	8.2.2

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	3.2	50	98.8	0.053	11	3.7	53862	53215		-3

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	3.2	3.31	94.4		0.907	1.1	3.5	4992

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	MIR	THROUGHOUT	3.228	50	53170	2697	97.86	0.292	0.292	0.29	0.306	0.3	RANDOM	115.697

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]
-1.52			-1.63		3.15

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.031
r_dihedral_angle_3_deg	18.539
r_dihedral_angle_4_deg	10.616
r_dihedral_angle_1_deg	6.023
r_angle_refined_deg	1.04
r_scangle_it	0.976
r_angle_other_deg	0.842
r_scbond_it	0.732
r_symmetry_vdw_refined	0.588
r_symmetry_vdw_other	0.521
r_mcangle_it	0.498
r_mcbond_it	0.378
r_nbd_refined	0.224
r_nbd_other	0.184
r_nbtor_refined	0.182
r_xyhbond_nbd_refined	0.149
r_mcbond_other	0.146
r_nbtor_other	0.086
r_symmetry_hbond_refined	0.083
r_chiral_restr	0.062
r_xyhbond_nbd_other	0.033
r_bond_refined_d	0.008
r_gen_planes_refined	0.003
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13538
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
SOLVE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
HKL-2000	data reduction