4HVJ | pdb_00004hvj

Crystal structure of a putative uncharacterized protein from Mycobacterium tuberculosis in complex with AMP

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4HEC

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7	290	EMBio JCSG+ G1 opt: 25% Jeffamine ED2003 pH 7.0, 100mM HEPES pH 7.0; MytuD.18400.a.A1.PS01434 at 25.6mg/m, soak and cryo: 35% Jeffamine ED2003, 100mM HEPES pH 7.0, 2.5M AMP, 2.5mM MgCl2 for 1 hour, VAPOR DIFFUSION, SITTING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
1.96	37

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.52	α = 90
b = 76.25	β = 90
c = 105.77	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+	Rigaku Varimax	2012-09-13	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)	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	50	99.3	0.079	20.87	6.9	20831	20675		-3	31.062

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	2.1	2.15	94.1		0.398	4.7

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	4HEC	2.1	43.49	20831	20630	1058	99.28	0.1799	0.1799	0.1774	0.19	0.2267	0.23	RANDOM	27.7637

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]
-0.73			-0.59		1.32

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.553
r_dihedral_angle_4_deg	19.846
r_dihedral_angle_3_deg	13.619
r_dihedral_angle_1_deg	5.595
r_angle_refined_deg	1.518
r_angle_other_deg	0.801
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.553
r_dihedral_angle_4_deg	19.846
r_dihedral_angle_3_deg	13.619
r_dihedral_angle_1_deg	5.595
r_angle_refined_deg	1.518
r_angle_other_deg	0.801
r_chiral_restr	0.081
r_bond_refined_d	0.011
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2567
Nucleic Acid Atoms
Solvent Atoms	167
Heterogen Atoms	25

Software

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

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.