Experiment: 3RIM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2R8O	model of Rv1449c with E. coli transketolase (pdb entry 2r8o) as template

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	5.5	293.15	17% PEG 10000, 0.1M ammonium acetate in 0.1M bis-tris, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.88

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 74.53	α = 82.2
b = 80.12	β = 81.16
c = 130.1	γ = 66.37

Symmetry
Space Group	P 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	MARMOSAIC 225 mm CCD		2009-10-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X06DA	0.979	SLS	X06DA

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	2.494	128.12	96.62				91429

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	2.49	2.64	91.16		0.59	0.431	2.77	3.9	13701

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	model of Rv1449c with E. coli transketolase (pdb entry 2r8o) as template	2.49	19.81	2.01	91429	86846	4579	96.69	0.22544	0.22298	0.2721	RANDOM	27.069

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]
0.91	0.21	-1.64	1	-0.24	-1.5

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.555
r_dihedral_angle_4_deg	22.458
r_dihedral_angle_3_deg	17.625
r_dihedral_angle_1_deg	6.235
r_scangle_it	2.603
r_angle_refined_deg	1.634
r_scbond_it	1.572
r_mcangle_it	1.064
r_mcbond_it	0.566
r_chiral_restr	0.097

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.555
r_dihedral_angle_4_deg	22.458
r_dihedral_angle_3_deg	17.625
r_dihedral_angle_1_deg	6.235
r_scangle_it	2.603
r_angle_refined_deg	1.634
r_scbond_it	1.572
r_mcangle_it	1.064
r_mcbond_it	0.566
r_chiral_restr	0.097
r_bond_refined_d	0.017
r_gen_planes_refined	0.007

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	21150
Nucleic Acid Atoms
Solvent Atoms	410
Heterogen Atoms	156

Software

Software
Software Name	Purpose
XDS	data scaling
PHASER	phasing
REFMAC	refinement
XDS	data reduction

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 R01GM133198.