3RD5 | pdb_00003rd5

Crystal structure of a putative uncharacterized protein from Mycobacterium Paratuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		STRUCTURE SOLVED VIA IODIDE PHASING AT CUKALPHA, DATA SET 2 WAS USED FOR THIS

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	EMERALDBIOSYSTEMS JCSG+ SCREEN B4: 100MM HEPES PH 7.5, 10% PEG 8000, 8% ETHYLENE GLYCOL, MYPAA.01249.CA1 PW29465 AT 29 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 290K.
2	VAPOR DIFFUSION, SITTING DROP	7.5	290	EMERALDBIOSYSTEMS JCSG+ SCREEN B4: 100MM HEPES PH 7.5, 10% PEG 8000, 8% ETHYLENE GLYCOL, MYPAA.01249.CA1 PW29465 AT 29 MG/ML, FOR PHASING THIS CRYSTAL WAS TRANFERRED IN 100MM HEPES PH 7.5, 15% PEG 6000, 10% ETHYLENE GLYCOL, 400MM SODIUM IODIDE, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 64.92	α = 90
b = 78.1	β = 90
c = 86.22	γ = 90

Symmetry
Space Group	P 21 21 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 300 mm CCD		2011-03-04	M	SINGLE WAVELENGTH
2	2	x-ray	100	CCD	RIGAKU SATURN 944+		2011-03-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 21-ID-G	0.978560	APS	21-ID-G
2	ROTATING ANODE	RIGAKU FR-E+ SUPERBRIGHT	1.5418

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	1.5	50	98.9	0.049	0.049	22.61	7.6	70109	70109		-3	22.7

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.5	1.54	100		0.389	0.389	4.4	5.4	5161

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	SAD	THROUGHOUT	STRUCTURE SOLVED VIA IODIDE PHASING AT CUKALPHA, DATA SET 2 WAS USED FOR THIS	1.5	49.92	70109	69906	3526	98.7	0.134	0.134	0.133	0.13	0.15	0.15	RANDOM	14.71

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]
-0.19			0.62		-0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.377
r_dihedral_angle_4_deg	17.028
r_dihedral_angle_3_deg	11.658
r_dihedral_angle_1_deg	5.525
r_scangle_it	4.028
r_scbond_it	2.491
r_mcangle_it	1.562
r_angle_refined_deg	1.539
r_angle_other_deg	1.019
r_mcbond_it	0.924
r_mcbond_other	0.259
r_chiral_restr	0.1
r_bond_refined_d	0.015
r_gen_planes_refined	0.009
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2031
Nucleic Acid Atoms
Solvent Atoms	413
Heterogen Atoms	19

Software

Software
Software Name	Purpose
CrystalClear	data collection
PHASER	phasing
REFMAC	refinement
XDS	data reduction
XSCALE	data scaling