3DU0 | pdb_00003du0

E. coli dihydrodipicolinate synthase with first substrate, pyruvate, bound in active site

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	hanging drop	10	277	1.8M K2HPO4, N-octyl-beta-(R)-glucopyranoside, pH 10, hanging drop, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.7	66.78

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.95	α = 90
b = 120.95	β = 90
c = 110.03	γ = 120

Symmetry
Space Group	P 31 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		IMAGE PLATE	RIGAKU RAXIS IV	OSMIC BLUE MIRRORS	2005-09-15	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	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	32.14	99.6	0.083	10.4	4.08		62822		3	25.2

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	MOLECULAR REPLACEMENT	THROUGHOUT	2	32.14	62813	3143	99.61	0.191	0.188	0.1901	0.245	0.2443	RANDOM	27.838

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.514
r_dihedral_angle_4_deg	17.64
r_dihedral_angle_3_deg	16.054
r_dihedral_angle_1_deg	7.562
r_scangle_it	4.769
r_scbond_it	3.37
r_mcangle_it	1.888
r_angle_refined_deg	1.221
r_mcbond_it	1.156
r_nbtor_refined	0.305

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.514
r_dihedral_angle_4_deg	17.64
r_dihedral_angle_3_deg	16.054
r_dihedral_angle_1_deg	7.562
r_scangle_it	4.769
r_scbond_it	3.37
r_mcangle_it	1.888
r_angle_refined_deg	1.221
r_mcbond_it	1.156
r_nbtor_refined	0.305
r_nbd_refined	0.228
r_symmetry_vdw_refined	0.214
r_symmetry_hbond_refined	0.165
r_xyhbond_nbd_refined	0.163
r_metal_ion_refined	0.103
r_chiral_restr	0.096
r_gen_planes_refined	0.012
r_bond_refined_d	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4390
Nucleic Acid Atoms
Solvent Atoms	522
Heterogen Atoms	26

Software

Software
Software Name	Purpose
d*TREK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
d*TREK	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.