2YHK

D214A mutant of tyrosine phenol-lyase from Citrobacter freundii

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2EZ1	PDB ENTRY 2EZ1

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	293	THE CRYSTALS WERE GROWN AT 293 K BY THE HANGING DROP VAPOR DIFFUSION TECHNIQUE BY MIXING 2 UL OF THE PROTEIN SOLUTION, 18-20 MG/ML, WITH AN EQUAL VOLUME OF THE RESERVOIR SOLUTION CONTAINING 50 MMOL/L TRIETHANOLAMINE BUFFER PH 8.0, 0.4-0.8 MOL/L KCL, 0.35-0.38 G/ML PEG 5000 MME, 5 MMOL/L PYRIDOXAL-5-PHOSPHATE, AND 2 MMOL/L DITHIOTHREITOL.

Crystal Properties
Matthews coefficient	Solvent content
2.7	55

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 132.605	α = 90
b = 142.705	β = 90
c = 59.412	γ = 90

Symmetry
Space Group	P 21 21 2

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	MARRESEARCH SX-165	MIRRORS	2005-05-02	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM30A		ESRF	BM30A

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	1.91	25	99	0.07	15	4.5		87110		-1	24.4

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)
1	1.91	1.97	99		0.5	3.1	4.2

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	FOURIER SYNTHESIS	THROUGHOUT	PDB ENTRY 2EZ1	1.91	25	85457	1283	98.56	0.15604	0.15571	0.17711	RANDOM	32.732

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]
-0.36			-1.58		1.94

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.425
r_dihedral_angle_4_deg	15.088
r_dihedral_angle_3_deg	14.206
r_dihedral_angle_1_deg	6.016
r_scangle_it	5.984
r_scbond_it	4.032
r_mcangle_it	2.259
r_mcbond_it	1.427
r_angle_refined_deg	1.393
r_chiral_restr	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7202
Nucleic Acid Atoms
Solvent Atoms	746
Heterogen Atoms	109

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	phasing