3HGB

Crystal structure of glycine cleavage system protein H from Mycobacterium tuberculosis

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	289	JCSG+ screen condition B11, 1.6M Na citrate, 27.2 mg/mL protein, tracking ID 202071b11, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

Crystal Properties
Matthews coefficient	Solvent content
2.19	43.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 86.86	α = 90
b = 51.47	β = 94.64
c = 32.53	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	RIGAKU SATURN 944+		2009-05-07	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	1.75	19.24	96.9	0.027	23.75			14091		-3	17.299

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	1.75	1.8	98.1		0.088	6.2		1067

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1onl	1.75	19.24	14091	710	96.87	0.183	0.181	0.22	RANDOM	12.298

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]
-0.07		-0.06	0.66		-0.6

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.437
r_dihedral_angle_4_deg	19.605
r_dihedral_angle_3_deg	10.416
r_dihedral_angle_1_deg	5.904
r_scangle_it	2.948
r_scbond_it	1.711
r_angle_refined_deg	1.185
r_mcangle_it	1.183
r_mcbond_it	0.614
r_chiral_restr	0.073

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	28.437
r_dihedral_angle_4_deg	19.605
r_dihedral_angle_3_deg	10.416
r_dihedral_angle_1_deg	5.904
r_scangle_it	2.948
r_scbond_it	1.711
r_angle_refined_deg	1.185
r_mcangle_it	1.183
r_mcbond_it	0.614
r_chiral_restr	0.073
r_bond_refined_d	0.008
r_gen_planes_refined	0.005

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	988
Nucleic Acid Atoms
Solvent Atoms	190
Heterogen Atoms

Software

Software
Software Name	Purpose
XSCALE	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.