4DXV | pdb_00004dxv

Crystal structure of Dihydrodipicolinate synthase from Acinetobacter baumannii complexed with Mg and Cl ions at 1.80 A resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3RK8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.2	298	0.2M MgCl2, PEG 3350, pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
2.37	48.01

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 51.35	α = 90
b = 122.47	β = 115.92
c = 52.33	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	77	CCD	MARRESEARCH	mirror	2011-10-30	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE BM14	0.97	ESRF	BM14

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	1.8	61.24	99.3	0.103	14.4		50787	50787

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)
1	1.8	1.83	98		0.56	2

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 (All)	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	3RK8	1.8	61.24	50787	50787	2720	99.55	0.15454	0.15454	0.15217	0.15	0.19875	0.2	RANDOM	17.073

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]
1.67		0.08	-0.64		-0.95

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.097
r_dihedral_angle_4_deg	15.555
r_dihedral_angle_3_deg	14.67
r_dihedral_angle_1_deg	6.221
r_scangle_it	6.054
r_scbond_it	3.801
r_angle_refined_deg	2.121
r_mcangle_it	2.048
r_mcbond_it	1.25
r_chiral_restr	0.164

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.097
r_dihedral_angle_4_deg	15.555
r_dihedral_angle_3_deg	14.67
r_dihedral_angle_1_deg	6.221
r_scangle_it	6.054
r_scbond_it	3.801
r_angle_refined_deg	2.121
r_mcangle_it	2.048
r_mcbond_it	1.25
r_chiral_restr	0.164
r_bond_refined_d	0.027
r_gen_planes_refined	0.012

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4390
Nucleic Acid Atoms
Solvent Atoms	637
Heterogen Atoms	9

Software

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