3ING

Crystal structure of Homoserine dehydrogenase (NP_394635.1) from THERMOPLASMA ACIDOPHILUM at 1.95 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.14	293	49.0000% 2-propanol, 5.0000% polyethylene glycol 1000, 0.1M citric acid pH 5.14, NANODROP, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.69	54.24

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 69.821	α = 90
b = 92.113	β = 90
c = 120.788	γ = 90

Symmetry
Space Group	C 2 2 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	MARMOSAIC 325 mm CCD	Flat collimating mirror, toroid focusing mirror	2009-03-19	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL9-2	0.91162,0.97927,0.97908	SSRL	BL9-2

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	1.95	28.105	98.6	0.079	8.45	3.65		28686		-3	20.319

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	1.95	2.02	97.2		0.499	1.6

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.95	28.105	28657	1435	99.6	0.154	0.152	0.193	RANDOM	28.208

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]
0.05			0.99		-1.04

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.7
r_dihedral_angle_4_deg	15.33
r_dihedral_angle_3_deg	11.692
r_scangle_it	7.159
r_dihedral_angle_1_deg	5.14
r_scbond_it	4.977
r_mcangle_it	3.113
r_mcbond_it	1.909
r_angle_refined_deg	1.623
r_angle_other_deg	1.12
r_mcbond_other	0.543
r_symmetry_vdw_other	0.311
r_nbd_refined	0.242
r_symmetry_vdw_refined	0.238
r_symmetry_hbond_refined	0.224
r_nbd_other	0.197
r_xyhbond_nbd_refined	0.188
r_nbtor_refined	0.182
r_nbtor_other	0.091
r_chiral_restr	0.078
r_xyhbond_nbd_other	0.027
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2405
Nucleic Acid Atoms
Solvent Atoms	214
Heterogen Atoms	73

Software

Software
Software Name	Purpose
REFMAC	refinement
PHENIX	refinement
SHELX	phasing
MolProbity	model building
XSCALE	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
SHARP	phasing