4HPJ | pdb_00004hpj

Crystal structure of Tryptophan Synthase at 1.45 A resolution in complex with 2-aminophenol quinonoid in the beta site and the F9 inhibitor in the alpha site

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1TJP

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.8	298	50 mM Bicine-CsOH, 10% PEG 8,000, 2 mM Spermine, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.59	52.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 184.329	α = 90
b = 59.716	β = 94.68
c = 67.527	γ = 90

Symmetry
Space Group	C 1 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	ADSC QUANTUM 315		2012-05-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 12.3.1	1.000	ALS	12.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.449	91.858	84.8	0.095	13.1	7.7	109585	109585		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.45	1.53	62.9		0.447	0.447	1.6	2.6	11872

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	1TJP	1.45	19.67	117892	109556	5519	84.55	0.1488	0.1488	0.1466	0.15	0.1893	0.19	RANDOM	19.7331

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]
-0.08		0.07	0.13		-0.05

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.538
r_sphericity_free	26.666
r_dihedral_angle_4_deg	16.758
r_dihedral_angle_3_deg	12.474
r_sphericity_bonded	11.528
r_dihedral_angle_1_deg	5.648
r_rigid_bond_restr	2.805
r_angle_refined_deg	1.453
r_chiral_restr	0.097
r_bond_refined_d	0.011

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.538
r_sphericity_free	26.666
r_dihedral_angle_4_deg	16.758
r_dihedral_angle_3_deg	12.474
r_sphericity_bonded	11.528
r_dihedral_angle_1_deg	5.648
r_rigid_bond_restr	2.805
r_angle_refined_deg	1.453
r_chiral_restr	0.097
r_bond_refined_d	0.011
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	5009
Nucleic Acid Atoms
Solvent Atoms	644
Heterogen Atoms	99

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

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.