3NA6 | pdb_00003na6

Crystal structure of a succinylglutamate desuccinylase (TM1040_2694) from SILICIBACTER SP. TM1040 at 2.00 A resolution

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	277	0.2000M NaCl, 30.0000% PEG-3000, 0.1M TRIS pH 7.0, 0.006 M Calcium Chloride, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.72	54.74

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.773	α = 90
b = 99.773	β = 90
c = 137.179	γ = 120

Symmetry
Space Group	P 63 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 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2010-03-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91837,0.97922,0.97905	SSRL	BL9-2

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	2	29.487	99.5	0.157	11.56			27876		-3	28.032

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)
	2	2.07	96.6		0.013	1.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	MAD	THROUGHOUT	2	29.487	27844	1397	99.74	0.163	0.161	0.17	0.195	0.2	RANDOM	29.563

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]
0.92	0.46		0.92		-1.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.242
r_dihedral_angle_4_deg	24.762
r_dihedral_angle_3_deg	14.023
r_scangle_it	7.279
r_dihedral_angle_1_deg	6.526
r_scbond_it	5.16
r_mcangle_it	2.817
r_mcbond_it	1.724
r_angle_refined_deg	1.513
r_angle_other_deg	0.894

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.242
r_dihedral_angle_4_deg	24.762
r_dihedral_angle_3_deg	14.023
r_scangle_it	7.279
r_dihedral_angle_1_deg	6.526
r_scbond_it	5.16
r_mcangle_it	2.817
r_mcbond_it	1.724
r_angle_refined_deg	1.513
r_angle_other_deg	0.894
r_mcbond_other	0.496
r_chiral_restr	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2493
Nucleic Acid Atoms
Solvent Atoms	313
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SOLVE	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction

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.