3K3D | pdb_00003k3d

The N-terminal PAS domain crystal structure of RV1364C from Mycobacterium Tuberculosis at 2.3 angstrom

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		MODEL BUILT FROM SELENIUM MAD

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8	292.16	1.4 M AMMONIUM SULFATE, 0.1 M TRIS- HCL, 0.1 M SODIUM CHLORIDE, pH 8.00, VAPOR DIFFUSION, HANGING DROP, temperature 292.16K

Crystal Properties
Matthews coefficient	Solvent content
2.66	53.82

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.137	α = 90
b = 60.137	β = 90
c = 171.948	γ = 120

Symmetry
Space Group	P 62 2 2

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		2006-03-20	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	EMBL/DESY, HAMBURG BEAMLINE BW7A	0.972	EMBL/DESY, HAMBURG	BW7A

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	2.3	20	100	0.079	39	21.3	8731	8731	1	1	59.7

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)
	2.3	2.34	100		0.733	4.62	22.8

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	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	MODEL BUILT FROM SELENIUM MAD	2.3	20	8685	8685	1226	98.9	0.251	0.251	0.243	0.2304	0.295	0.2759	RANDOM	58.53

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]
3.02	1.51		3.02		-4.53

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.786
r_dihedral_angle_4_deg	20.219
r_dihedral_angle_3_deg	19.52
r_dihedral_angle_1_deg	8.215
r_scangle_it	4.491
r_scbond_it	2.905
r_angle_refined_deg	1.315
r_mcangle_it	1.113
r_mcbond_it	0.633
r_nbtor_refined	0.304

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.786
r_dihedral_angle_4_deg	20.219
r_dihedral_angle_3_deg	19.52
r_dihedral_angle_1_deg	8.215
r_scangle_it	4.491
r_scbond_it	2.905
r_angle_refined_deg	1.315
r_mcangle_it	1.113
r_mcbond_it	0.633
r_nbtor_refined	0.304
r_symmetry_hbond_refined	0.295
r_symmetry_vdw_refined	0.205
r_nbd_refined	0.2
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.099
r_bond_refined_d	0.011
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1025
Nucleic Acid Atoms
Solvent Atoms	20
Heterogen Atoms

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.