6XGS | pdb_00006xgs

Crystal Structure of Dihydrodipicolinate synthase (DHDPS) from Brucella suis 1330

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4I7U	PDB entry 4i7u as per MORDA

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.5	287	Qiagen JCSG Core-1 screen, f12: 40% (V/V) MPD, 100mM sodium phosphate dibasic / citric acid pH 4.2: BrsuA.01563.a.A1.PW34594; tray 231309f12, cryo, 20%EG, puck atd2-7

Crystal Properties
Matthews coefficient	Solvent content
2.29	46.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.65	α = 90
b = 86.65	β = 90
c = 142.97	γ = 120

Symmetry
Space Group	P 32

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	ADSC QUANTUM 315r	Si(220)	2012-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 5.0.1	0.97740	ALS	5.0.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	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	2.2	43.33	99.1	0.125	0.141	0.993	11.74	4.633		60445			28.674

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.2	2.26	98.2		0.566	0.639	0.804	2.64	4.626

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB entry 4i7u as per MORDA	2.2	43.33	58503	1935	99.14	0.1357	0.1348	0.16	0.162	0.18	RANDOM	20.617

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]
-21.39			-21.39		42.78

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.24
r_dihedral_angle_4_deg	16.131
r_dihedral_angle_3_deg	13.85
r_dihedral_angle_1_deg	6.723
r_angle_refined_deg	1.625
r_angle_other_deg	1.346
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.24
r_dihedral_angle_4_deg	16.131
r_dihedral_angle_3_deg	13.85
r_dihedral_angle_1_deg	6.723
r_angle_refined_deg	1.625
r_angle_other_deg	1.346
r_chiral_restr	0.076
r_bond_refined_d	0.011
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8786
Nucleic Acid Atoms
Solvent Atoms	452
Heterogen Atoms	77

Software

Software
Software Name	Purpose
XDS	data reduction
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MoRDa	phasing
Coot	model building

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.