3BAF | pdb_00003baf

Crystal structure of shikimate kinase from Mycobacterium tuberculosis in complex with AMP-PNP

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8	293	PEG, pH8, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
3.43	64.15

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 67.297	α = 90
b = 67.297	β = 90
c = 97.692	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	CCD	MAR CCD 165 mm		2007-04-17	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)	R Merge I (Observed)	R Sym 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	2.25	37.42	99.8	0.19	0.13	25.8	3.5		12600	2	2	35.1

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)
	2.25	2.37	100		0.19		3.4	1816

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	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 1ZYU	2.25	37.42	2	12580	11983	597	99.72	0.21009	0.20651	0.21	0.28397	0.28	RANDOM	34.889

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]
0.82	0.41		0.82		-1.23

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.229
r_dihedral_angle_4_deg	20.338
r_dihedral_angle_3_deg	18.056
r_dihedral_angle_1_deg	7.849
r_scangle_it	5.828
r_scbond_it	4.041
r_angle_refined_deg	3.034
r_mcbond_it	2.351
r_mcangle_it	2.348
r_symmetry_hbond_refined	0.526

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.229
r_dihedral_angle_4_deg	20.338
r_dihedral_angle_3_deg	18.056
r_dihedral_angle_1_deg	7.849
r_scangle_it	5.828
r_scbond_it	4.041
r_angle_refined_deg	3.034
r_mcbond_it	2.351
r_mcangle_it	2.348
r_symmetry_hbond_refined	0.526
r_xyhbond_nbd_refined	0.377
r_nbtor_refined	0.277
r_nbd_refined	0.223
r_chiral_restr	0.189
r_symmetry_vdw_refined	0.179
r_bond_refined_d	0.039
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1226
Nucleic Acid Atoms
Solvent Atoms	136
Heterogen Atoms	43

Software

Software
Software Name	Purpose
REFMAC	refinement
MAR345dtb	data collection
MOSFLM	data reduction
SCALA	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.