3TK2 | pdb_00003tk2

Crystallographic structure of phenylalanine hydroxylase from Chromobacterium violaceum cocrystallized with phenylalanine in a site distal to the active site

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	293	0.1M Na-HEPES, 0.001M Magnesium chloride hexahydrate, 0.005M Nickel (II) chloride hexahydrate, 15% w/v PEG 3,350, 0.1M hexammine cobalt (II) chloride, 1.0M guanidine hydrochloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.79

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.934	α = 76.56
b = 38.561	β = 72.9
c = 47.8	γ = 85.41

Symmetry
Space Group	P 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	IMAGE PLATE	MAR scanner 300 mm plate		2011-06-26	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 23-ID-D	1.033	APS	23-ID-D

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.35	50	93.5	0.043	0.043	34.2	3.9	50401	47843	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.35	1.37	84

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 (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 1LTU	1.35	24.49	51027	47125	2557	93.76	0.16098	0.15853	0.2	0.20727	0.24	RANDOM	15.028

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]
	0.01		0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.425
r_dihedral_angle_4_deg	14.964
r_dihedral_angle_3_deg	14.706
r_sphericity_free	10.968
r_sphericity_bonded	6.862
r_dihedral_angle_1_deg	6.047
r_scangle_it	6.038
r_scbond_it	4.489
r_mcangle_it	3.409
r_rigid_bond_restr	2.625

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.425
r_dihedral_angle_4_deg	14.964
r_dihedral_angle_3_deg	14.706
r_sphericity_free	10.968
r_sphericity_bonded	6.862
r_dihedral_angle_1_deg	6.047
r_scangle_it	6.038
r_scbond_it	4.489
r_mcangle_it	3.409
r_rigid_bond_restr	2.625
r_mcbond_it	2.422
r_angle_refined_deg	2.199
r_chiral_restr	0.144
r_bond_refined_d	0.025
r_gen_planes_refined	0.014

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2220
Nucleic Acid Atoms
Solvent Atoms	283
Heterogen Atoms	14

Software

Software
Software Name	Purpose
HKL-3000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling

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.