1VLC

Crystal structure of 3-isopropylmalate dehydrogenase (TM0556) from Thermotoga maritima at 1.90 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	9	277	25.0% PEG-4000, 0.2M Li2SO4, 0.1M TRIS pH 9.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K
2	VAPOR DIFFUSION,SITTING DROP,NANODROP	7.5	277	20.0% PEG-8000, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.62
2.91	57.34

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 118.78	α = 90
b = 118.78	β = 90
c = 56.699	γ = 120

Symmetry
Space Group	P 3 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	100	CCD	ADSC QUANTUM 315	flat mirror	2004-06-27	M	SINGLE WAVELENGTH
2	1	x-ray	100	M	MAD
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1
2	SYNCHROTRON	SSRL BEAMLINE BL11-1	0.979251, 0.979508, 0.885567	SSRL	BL11-1

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	1.9	41.01	99.5	0.11	13.6	5.6		36394			39.46

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	1.9	1.95	97.2		0.684	1.9	3.6	2598

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	1.9	41.01	34079	1801	98.15	0.18934	0.18779	0.21822	RANDOM	30.46

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]
1.45	0.73		1.45		-2.18

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.297
r_dihedral_angle_4_deg	19.243
r_dihedral_angle_3_deg	13.779
r_scangle_it	8.908
r_scbond_it	6.495
r_dihedral_angle_1_deg	6.197
r_mcangle_it	3.795
r_mcbond_it	2.902
r_angle_refined_deg	1.673
r_angle_other_deg	0.872
r_mcbond_other	0.748
r_symmetry_vdw_other	0.219
r_nbd_refined	0.211
r_nbd_other	0.178
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.164
r_symmetry_vdw_refined	0.146
r_symmetry_hbond_refined	0.129
r_chiral_restr	0.109
r_nbtor_other	0.087
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2723
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	1

Software

Software
Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
SHELX	model building
autoSHARP	phasing
SOLOMON	phasing
REFMAC	refinement
CCP4	data scaling
SHELX	phasing