3PCO | pdb_00003pco

crystal structure of E. coli phenylalanine-tRNA synthetase complexed with phenylalanine and AMP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1PYS	PDB entry code 1PYS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	293	17%-20% PEG 8000K, 0.2 M MgCl2, 0.1 M Tris, VAPOR DIFFUSION, HANGING DROP, temperature 293K, pH 8.5

Crystal Properties
Matthews coefficient	Solvent content
3	58.94

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.547	α = 90
b = 178.936	β = 90
c = 254.417	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 315r		2009-10-12	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.97620	ESRF	ID14-4

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	3	38.71	99.2	0.112	6.6	4.4	5749	58932

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)
	3	3.11	98.3		0.808		3.8	5749

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry code 1PYS	3.02	38.71	5749	58880	2981	98.36	0.2352	0.2352	0.2317	0.27	0.2998	0.26	RANDOM	91.794

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]
3.52			1.6		-5.13

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.405
r_dihedral_angle_3_deg	23.899
r_dihedral_angle_4_deg	20.144
r_dihedral_angle_1_deg	9.261
r_scangle_it	2.261
r_angle_refined_deg	1.811
r_scbond_it	1.286
r_mcangle_it	0.934
r_mcbond_it	0.486
r_chiral_restr	0.135

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.405
r_dihedral_angle_3_deg	23.899
r_dihedral_angle_4_deg	20.144
r_dihedral_angle_1_deg	9.261
r_scangle_it	2.261
r_angle_refined_deg	1.811
r_scbond_it	1.286
r_mcangle_it	0.934
r_mcbond_it	0.486
r_chiral_restr	0.135
r_bond_refined_d	0.014
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	16654
Nucleic Acid Atoms
Solvent Atoms
Heterogen Atoms	70

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.