1VS0 | pdb_00001vs0

Crystal Structure of the Ligase Domain from M. tuberculosis LigD at 2.4A

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	294	6% PEG 3000, 25 mM ZnCl2, 100 mM sodium acetate (pH 4.6), VAPOR DIFFUSION, HANGING DROP, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.5	50.77

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 57.102	α = 90
b = 57.102	β = 90
c = 368.957	γ = 120

Symmetry
Space Group	P 32 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 4		2004-09-23	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.9796, 1.020, 0.9798	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	50	99.5	0.082	18.8	5.3	28934	28772	1	1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.4	2.49	96.2		0.35	2.9	3.2	5147

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	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	MAD	THROUGHOUT	2.4	50	28934	28487	1453	99.09	0.195	0.195	0.192	0.1866	0.248	0.2453	RANDOM	36.715

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]
1.01	0.51		1.01		-1.52

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.015
r_dihedral_angle_4_deg	19.204
r_dihedral_angle_3_deg	18.654
r_dihedral_angle_1_deg	6.814
r_mcangle_it	3.715
r_scangle_it	3.07
r_mcbond_it	2.497
r_scbond_it	2.281
r_angle_refined_deg	1.6
r_symmetry_hbond_refined	0.352
r_nbtor_refined	0.311
r_metal_ion_refined	0.309
r_symmetry_vdw_refined	0.268
r_nbd_refined	0.233
r_xyhbond_nbd_refined	0.213
r_symmetry_metal_ion_refined	0.137
r_chiral_restr	0.104
r_bond_refined_d	0.014
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4777
Nucleic Acid Atoms
Solvent Atoms	407
Heterogen Atoms	9

Software

Software
Software Name	Purpose
Blu-Ice	data collection
HKL-2000	data reduction
SOLVE	phasing
REFMAC	refinement
HKL-2000	data scaling