4HEC | pdb_00004hec

Crystal structure of a putative uncharacterized protein from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	Other		de novo phasing with iodide ions

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	290	EMBio JCSG+ B4: 10% PEG 8000, 8% Ethylene glycol, 100mM HEPES pH 7.5; MytuD.18400.a.A1.PS01434 at 12.8mg/ml + 2.5mM AMPPNP and MgCl2, cryo: 20% EG; the structure was solved via iodide SAD: a crystal was soaked in reservoir plus 20% ethylene glycol and 750mM NaI, anomalous amplitudes are deposited, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
1.99	38

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.78	α = 90
b = 76.72	β = 90
c = 106.04	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	RIGAKU SATURN 944+		2012-08-31	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	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	1.8	50	99.1	0.036	0.036	27.29	4.7	33216	32926		-3	28.69

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	1.8	1.85	96.4		0.434	2.44

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	de novo phasing with iodide ions	1.8	38.39	33216	31227	1645	99.15	0.1904	0.1904	0.1884	0.1968	0.2277	0.2373	RANDOM	25.3846

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]
-0.68			0.01		0.67

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	29.271
r_dihedral_angle_4_deg	22.951
r_dihedral_angle_3_deg	11.828
r_dihedral_angle_1_deg	5.6
r_angle_refined_deg	1.652
r_angle_other_deg	0.86
r_chiral_restr	0.094
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2570
Nucleic Acid Atoms
Solvent Atoms	220
Heterogen Atoms	2

Software

Software
Software Name	Purpose
XSCALE	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
StructureStudio	data collection