3C0J

Structure of E. coli dihydrodipicolinate synthase complexed with hydroxypyruvate

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	10	285	1.8M K2HPO4 (pH 10.0), 6% w/v N-octyl-D-glucopyranoside, VAPOR DIFFUSION, HANGING DROP, temperature 285K

Crystal Properties
Matthews coefficient	Solvent content
3.73	67.04

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.967	α = 90
b = 120.967	β = 90
c = 110.639	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	110	IMAGE PLATE	RIGAKU RAXIS IV++		2006-08-01	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	2.4	34.79	98.5	0.114	7.8	3.96	36400	36400

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	2.4	2.49	98.9		0.393	2.8

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 1YXC	2.4	31.49	34563	1818	100	0.1734	0.1702	0.23729	RANDOM	32.2

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]
-0.35	-0.17		-0.35		0.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.619
r_dihedral_angle_4_deg	18.22
r_dihedral_angle_3_deg	16.412
r_dihedral_angle_1_deg	7.041
r_scangle_it	4.12
r_scbond_it	2.674
r_angle_refined_deg	1.765
r_mcangle_it	1.471
r_angle_other_deg	1.095
r_mcbond_it	0.789
r_symmetry_vdw_other	0.293
r_symmetry_hbond_refined	0.231
r_symmetry_vdw_refined	0.227
r_nbd_refined	0.222
r_nbd_other	0.205
r_mcbond_other	0.182
r_nbtor_refined	0.172
r_xyhbond_nbd_refined	0.165
r_metal_ion_refined	0.148
r_chiral_restr	0.099
r_nbtor_other	0.093
r_bond_refined_d	0.021
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4360
Nucleic Acid Atoms
Solvent Atoms	465
Heterogen Atoms	30

Software

Software
Software Name	Purpose
REFMAC	refinement
CrystalClear	data collection
d*TREK	data reduction
d*TREK	data scaling
AMoRE	phasing