3K3C | pdb_00003k3c

The N-terminal PAS domain crystal structure of Rv1364c from Mycobacterium tuberculosis at 1.62

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	292.16	1.4 M ammonium sulphate, 0.1 M Tris-HCl, 0.1 M sodium chloride, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 292.16K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 209.069	α = 90
b = 63.823	β = 89.95
c = 61.305	γ = 90

Symmetry
Space Group	C 1 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	MAR CCD 165 mm		2006-08-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE X13	0.808	EMBL/DESY, HAMBURG	X13

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	1.62	20	98.6	0.087	9	5	101268	101268	1	1	25.2

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)
	1.62	1.65	95.3		0.654	2.77	4.9	4886

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	MOLECULAR REPLACEMENT	THROUGHOUT	1.62	20	98602	93675	4927	96.11	0.183	0.183	0.181	0.19	0.21233	0.22	RANDOM	19.173

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]
0.34			0.45		-0.79

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.965
r_dihedral_angle_4_deg	17.686
r_dihedral_angle_3_deg	13.764
r_dihedral_angle_1_deg	5.415
r_scangle_it	4.315
r_scbond_it	3.206
r_angle_refined_deg	1.437
r_mcangle_it	1.433
r_mcbond_it	1.177
r_angle_other_deg	1.123
r_symmetry_vdw_other	0.26
r_nbd_refined	0.219
r_nbd_other	0.218
r_mcbond_other	0.19
r_nbtor_refined	0.186
r_symmetry_hbond_refined	0.181
r_chiral_restr	0.165
r_xyhbond_nbd_refined	0.163
r_symmetry_vdw_refined	0.16
r_nbtor_other	0.085
r_bond_refined_d	0.012
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4824
Nucleic Acid Atoms
Solvent Atoms	657
Heterogen Atoms	132

Software

Software
Software Name	Purpose
DENZO	data reduction
Auto-Rickshaw	phasing
REFMAC	refinement
SCALEPACK	data scaling