3FLU

Crystal structure of dihydrodipicolinate synthase from the pathogen Neisseria meningitidis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1YXC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.3	291	1.8M ammonium sulfate, 100mM Bis-Tris.HCl, pH 5.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.44	49.66

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 80.667	α = 90
b = 115.684	β = 90
c = 132.122	γ = 90

Symmetry
Space Group	P 21 21 21

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 315		2008-10-23	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	DIAMOND BEAMLINE I02	0.9796	Diamond	I02

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	1.999	115.684	99.9	0.096		5.7	84335	84251			21.23

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	2.07	100		0.349		5.7	8359

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 (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1YXC	2	115.47	84324	84214	4201	99.87	0.151	0.148	0.191	RANDOM	20.562

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]
0.34			-0.7		0.36

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.065
r_dihedral_angle_4_deg	16.803
r_dihedral_angle_3_deg	12.642
r_dihedral_angle_1_deg	6.825
r_scangle_it	6.212
r_scbond_it	4.421
r_mcangle_it	2.259
r_mcbond_it	1.726
r_angle_refined_deg	1.133
r_nbtor_refined	0.309

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.065
r_dihedral_angle_4_deg	16.803
r_dihedral_angle_3_deg	12.642
r_dihedral_angle_1_deg	6.825
r_scangle_it	6.212
r_scbond_it	4.421
r_mcangle_it	2.259
r_mcbond_it	1.726
r_angle_refined_deg	1.133
r_nbtor_refined	0.309
r_symmetry_vdw_refined	0.242
r_nbd_refined	0.213
r_symmetry_hbond_refined	0.179
r_xyhbond_nbd_refined	0.137
r_chiral_restr	0.09
r_gen_planes_refined	0.012
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	8722
Nucleic Acid Atoms
Solvent Atoms	938
Heterogen Atoms	264

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DNA	data collection
DENZO	data reduction
SCALEPACK	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.