4TWE

Structure of ligand-free N-acetylated-alpha-linked-acidic-dipeptidase like protein (NAALADaseL)

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP		293	0.16 M magnesium formate and 16% (w/v) PEG 3350, pH not adjusted

Crystal Properties
Matthews coefficient	Solvent content
2.76	55.37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 98.512	α = 90
b = 174.844	β = 90
c = 208.034	γ = 90

Symmetry
Space Group	I 2 2 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	MARMOSAIC 225 mm CCD		2009-06-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-BM	1.000	APS	22-BM

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	1.75	30	99.7	0.081	9	7.6		177979		-3

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	1.75	1.78	99.4		0.506		7.5	8822

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	MOLECULAR REPLACEMENT	THROUGHOUT	2PVW	1.75	29.14	176202	1757	98.41	0.1676	0.1674	0.1875	RANDOM	26.631

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]
-0.02			0.02		0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.966
r_dihedral_angle_4_deg	14.695
r_dihedral_angle_3_deg	12.28
r_dihedral_angle_1_deg	6.293
r_scangle_it	4.448
r_scbond_it	2.754
r_mcangle_it	1.742
r_angle_refined_deg	1.738
r_mcbond_it	1.015
r_chiral_restr	0.128

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.966
r_dihedral_angle_4_deg	14.695
r_dihedral_angle_3_deg	12.28
r_dihedral_angle_1_deg	6.293
r_scangle_it	4.448
r_scbond_it	2.754
r_mcangle_it	1.742
r_angle_refined_deg	1.738
r_mcbond_it	1.015
r_chiral_restr	0.128
r_bond_refined_d	0.02
r_gen_planes_refined	0.011

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	10908
Nucleic Acid Atoms
Solvent Atoms	1633
Heterogen Atoms	317

Software

Software
Software Name	Purpose
HKL-2000	data reduction
SERGUI	data collection
HKL-2000	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
Coot	model building
WARP	model building
PHASER	phasing

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 R01GM133198.