4ZAJ | pdb_00004zaj

2.2 Angstrom Crystal Structure of a Human Arginyl-tRNA Synthetase

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4Q2T

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	293	25% PEG 1000

Crystal Properties
Matthews coefficient	Solvent content
2.63	53.17

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 54.72	α = 90
b = 61.92	β = 90
c = 208.47	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	IMAGE PLATE	MAR scanner 300 mm plate		2015-03-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.97857	APS	21-ID-G

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	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	2.22	38.16	100	0.13	0.053	12.2	7.5		35995			26.204

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rpim I (All)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.22	2.28	100		0.681	0.294	2.9	6.9	2612

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work (Depositor)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	4Q2T	2.22	38.16	34130	1801	99.93	0.2211	0.2189	0.2643	0.2507	RANDOM	33.206

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]
1.1			-2.15		1.06

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.056
r_dihedral_angle_4_deg	18.504
r_dihedral_angle_3_deg	14.904
r_dihedral_angle_1_deg	5.986
r_mcangle_it	3.358
r_mcbond_it	1.959
r_mcbond_other	1.953
r_angle_refined_deg	1.318
r_angle_other_deg	0.935
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4638
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
xia2	data scaling
PHASER	phasing
PDB_EXTRACT	data extraction
xia2	data reduction