1YXC

Structure of E. coli dihydrodipicolinate synthase to 1.9 A

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	10	276	1.8M potassium phosphate, pH 10, VAPOR DIFFUSION, HANGING DROP, temperature 276K

Crystal Properties
Matthews coefficient	Solvent content
3.71	66.86

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.869	α = 90
b = 120.869	β = 90
c = 110.194	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		2004-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	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	1.9	39.57	99.7	0.089	9.7	4.3		73225	2	2

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)
	1.9	1.97	99.9		0.358	3.5	4.17

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	1dhp	1.9	39.56	69522	3700	100	0.17371	0.17175	0.21145	RANDOM	19.915

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]
-0.11	-0.06		-0.11		0.17

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.585
r_dihedral_angle_4_deg	18.511
r_dihedral_angle_3_deg	15.108
r_dihedral_angle_1_deg	6.439
r_scangle_it	3.885
r_scbond_it	2.381
r_angle_refined_deg	1.57
r_mcangle_it	1.343
r_angle_other_deg	0.901
r_mcbond_it	0.754
r_symmetry_vdw_other	0.233
r_nbd_refined	0.232
r_mcbond_other	0.209
r_symmetry_vdw_refined	0.199
r_nbd_other	0.187
r_nbtor_refined	0.171
r_xyhbond_nbd_refined	0.16
r_symmetry_hbond_refined	0.159
r_metal_ion_refined	0.124
r_chiral_restr	0.102
r_nbtor_other	0.094
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d	0.001
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	4304
Nucleic Acid Atoms
Solvent Atoms	616
Heterogen Atoms	4

Software

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