3FW0

Structure of Peptidyl-alpha-hydroxyglycine alpha-Amidating Lyase (PAL) bound to alpha-hydroxyhippuric acid (non-peptidic substrate)

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		PALcc native, being deposited at the same time as this structure

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.8	293	0.1M sodium acetate pH=4.8, 0.5mM mercury(II) acetate - 0.2ml mother liquor in reservoir. Then, crystals soaked in 5mM hydroxyhippuric acid for several hours, VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.56	51.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.93	α = 90
b = 75.08	β = 90
c = 97.026	γ = 90

Symmetry
Space Group	P 21 21 21

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	MAR CCD 165 mm	Monochromator Kohzu HLD-4 Double Crystal	2008-07-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 31-ID	1.00724	APS	31-ID

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	2.5	59.34	99.6	0.075	23.5	6.8	13347	13347

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	2.5	2.59	98.9		0.48	2.7	5.7	1306

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PALcc native, being deposited at the same time as this structure	2.52	59.34	13347	12648	655	99.09	0.20939	0.20672	0.26019	RANDOM	44.912

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]
1.12			0.24		-1.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.247
r_dihedral_angle_4_deg	19.785
r_dihedral_angle_3_deg	17.925
r_dihedral_angle_1_deg	7.552
r_angle_refined_deg	1.246
r_scangle_it	1.237
r_scbond_it	1.213
r_mcangle_it	0.541
r_nbtor_refined	0.31
r_mcbond_it	0.31

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.247
r_dihedral_angle_4_deg	19.785
r_dihedral_angle_3_deg	17.925
r_dihedral_angle_1_deg	7.552
r_angle_refined_deg	1.246
r_scangle_it	1.237
r_scbond_it	1.213
r_mcangle_it	0.541
r_nbtor_refined	0.31
r_mcbond_it	0.31
r_symmetry_hbond_refined	0.224
r_nbd_refined	0.195
r_symmetry_vdw_refined	0.167
r_xyhbond_nbd_refined	0.126
r_chiral_restr	0.115
r_bond_refined_d	0.008
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2619
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	17

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	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.