3TCY | pdb_00003tcy

Crystallographic structure of phenylalanine hydroxylase from Chromobacterium violaceum (cPAH) bound to 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
1.83	32.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 36.674	α = 76.65
b = 38.281	β = 73.03
c = 47.736	γ = 85.69

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	1.55	50	95	0.036	0.036	26.2	2.3	33011	31363	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	1.55	1.58	84.6

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	1.55	37.25	33090	31360	1647	94.78	0.16488	0.16266	0.18	0.20698	0.22	RANDOM	17.555

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	0.02

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.17
r_dihedral_angle_3_deg	14.353
r_dihedral_angle_4_deg	13.828
r_dihedral_angle_1_deg	5.298
r_sphericity_free	4.046
r_scangle_it	3.824
r_sphericity_bonded	2.808
r_scbond_it	2.549
r_mcangle_it	1.671
r_rigid_bond_restr	1.447

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.17
r_dihedral_angle_3_deg	14.353
r_dihedral_angle_4_deg	13.828
r_dihedral_angle_1_deg	5.298
r_sphericity_free	4.046
r_scangle_it	3.824
r_sphericity_bonded	2.808
r_scbond_it	2.549
r_mcangle_it	1.671
r_rigid_bond_restr	1.447
r_angle_refined_deg	1.4
r_mcbond_it	1.025
r_chiral_restr	0.091
r_bond_refined_d	0.011
r_gen_planes_refined	0.008

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2221
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	22

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.