2DFN | pdb_00002dfn

Structure of shikimate kinase from Mycobacterium tuberculosis complexed with ADP and shikimate at 1.9 angstrons of resolution

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1WE2	PDB ENTRY 1WE2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	293	0.1M tris-HCl, 17% PEG 1500, 0.5-0.7M LiCl, pH 8.0, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.84	56.76

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 63.296	α = 90
b = 63.296	β = 90
c = 91.61	γ = 120

Symmetry
Space Group	P 32 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	IMAGE PLATE	RIGAKU		2005-06-07	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	LNLS BEAMLINE D03B-MX1	1.427	LNLS	D03B-MX1

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	1.93	35.16	99	4.8		16169	16017	2	2

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.93	2.03	21.6			4.6	2160

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 (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	PDB ENTRY 1WE2	1.93	35.16	2	16475	15130	804	96.72	0.20494	0.202	0.2017	0.2	0.26687	0.26	RANDOM	32.718

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	31.012
r_dihedral_angle_3_deg	19.884
r_dihedral_angle_4_deg	19.472
r_scangle_it	9.333
r_dihedral_angle_1_deg	8.385
r_scbond_it	7.39
r_mcangle_it	4.917
r_mcbond_it	3.937
r_angle_refined_deg	2.01
r_symmetry_hbond_refined	0.555

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.012
r_dihedral_angle_3_deg	19.884
r_dihedral_angle_4_deg	19.472
r_scangle_it	9.333
r_dihedral_angle_1_deg	8.385
r_scbond_it	7.39
r_mcangle_it	4.917
r_mcbond_it	3.937
r_angle_refined_deg	2.01
r_symmetry_hbond_refined	0.555
r_xyhbond_nbd_refined	0.423
r_nbd_refined	0.361
r_symmetry_vdw_refined	0.35
r_nbtor_refined	0.319
r_chiral_restr	0.187
r_bond_refined_d	0.015
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1226
Nucleic Acid Atoms
Solvent Atoms	192
Heterogen Atoms	40

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
CCP4	data scaling
AMoRE	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.