3VAB

Crystal structure of Diaminopimelate decarboxylase from Brucella melitensis bound to PLP

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	289	BrmeA.00771.a.A1 PS01273 at 36.9 mg/mL against JCSG+ E2 0.2 M sodium chloride, 0.1 M sodium cacodylate pH 6.5, 2 M ammonium sulfate with 10 then 20% ethylene glycol as step cryo-protectant, crystal tracking ID 228027e2, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.45	49.85

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 59.53	α = 90
b = 126.37	β = 112.71
c = 68.18	γ = 90

Symmetry
Space Group	P 1 21 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	CCD	RIGAKU SATURN 944+	VariMax	2011-12-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

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	2.1	50	98.8	0.077	12.53	3.6	54306	53634		-3	22.068

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	2.1	2.15	93.7		0.174	5.97	2.9	4020

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	pdb entry 3n2b	2.1	50	53634	2737	98.94	0.2236	0.2212	0.2675	RANDOM	19.4125

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]
0.11		-0.6	-0.85		0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.772
r_dihedral_angle_4_deg	20.668
r_dihedral_angle_3_deg	13.423
r_dihedral_angle_1_deg	6.382
r_angle_refined_deg	1.593
r_angle_other_deg	1.105
r_chiral_restr	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.003

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	33.772
r_dihedral_angle_4_deg	20.668
r_dihedral_angle_3_deg	13.423
r_dihedral_angle_1_deg	6.382
r_angle_refined_deg	1.593
r_angle_other_deg	1.105
r_chiral_restr	0.088
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.003
r_gen_planes_other	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6388
Nucleic Acid Atoms
Solvent Atoms	725
Heterogen Atoms	17

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection
XDS	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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.