3TK4 | pdb_00003tk4

Crystal structure of phenylalanine hydroxylase from Chromobacterium violaceum bound to cobalt

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, 15% w/v PEG 3,350, 0.1M Hexammine cobalt (III) chloride, 1.0M Guanidine hydrochloride, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.86	33.91

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.885	α = 76.49
b = 38.577	β = 73.15
c = 47.877	γ = 85.39

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		2011-03-27	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	1.5	50	95.1	0.031	0.031	24.2	1.9		37372	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	1.5	1.53	82.5

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	1.5	37.51	37348	35492	1875	95.03	0.17275	0.17087	0.2	0.20965	0.24	RANDOM	15.696

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.642
r_dihedral_angle_3_deg	14.077
r_dihedral_angle_4_deg	13.631
r_dihedral_angle_1_deg	5.384
r_scangle_it	3.77
r_sphericity_free	3.653
r_sphericity_bonded	2.596
r_scbond_it	2.501
r_mcangle_it	1.72
r_rigid_bond_restr	1.404

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.642
r_dihedral_angle_3_deg	14.077
r_dihedral_angle_4_deg	13.631
r_dihedral_angle_1_deg	5.384
r_scangle_it	3.77
r_sphericity_free	3.653
r_sphericity_bonded	2.596
r_scbond_it	2.501
r_mcangle_it	1.72
r_rigid_bond_restr	1.404
r_angle_refined_deg	1.324
r_mcbond_it	1.012
r_chiral_restr	0.088
r_bond_refined_d	0.01
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2220
Nucleic Acid Atoms
Solvent Atoms	181
Heterogen Atoms	2

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.