Experiment: 2PKM

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2PKF	apo MTB ADK

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	290	Crystals were obtained in conditions containing 0.1 M HEPES-Na, pH 7.5 and 1.4 M trisodium citrate dihydrate, VAPOR DIFFUSION, HANGING DROP, temperature 290K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 71.9	α = 90
b = 71.9	β = 90
c = 110.8	γ = 120

Symmetry
Space Group	P 31 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	120	IMAGE PLATE	RIGAKU RAXIS IV	Osmic mirrors	2006-03-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	OTHER	1.5412

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	1.9	62.66	97.84	0.04			24855	24855

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.9	1.949	97.33

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	apo MTB ADK	1.9	62.26	24855	1299	97.84	0.21935	0.21723	0.25956	RANDOM	41.134

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]
0.01			0.01		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.423
r_dihedral_angle_4_deg	17.533
r_dihedral_angle_3_deg	13.83
r_dihedral_angle_1_deg	6.091
r_scangle_it	5.746
r_scbond_it	4.331
r_mcangle_it	3.308
r_mcbond_it	2.458
r_angle_refined_deg	1.336
r_nbtor_refined	0.3

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	36.423
r_dihedral_angle_4_deg	17.533
r_dihedral_angle_3_deg	13.83
r_dihedral_angle_1_deg	6.091
r_scangle_it	5.746
r_scbond_it	4.331
r_mcangle_it	3.308
r_mcbond_it	2.458
r_angle_refined_deg	1.336
r_nbtor_refined	0.3
r_symmetry_hbond_refined	0.226
r_symmetry_vdw_refined	0.204
r_nbd_refined	0.2
r_xyhbond_nbd_refined	0.133
r_chiral_restr	0.101
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2444
Nucleic Acid Atoms
Solvent Atoms	225
Heterogen Atoms	19

Software

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

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.