3ORT | pdb_00003ort

Mycobacterium tuberculosis PknB kinase domain L33D mutant (crystal form 6)

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MRU	PDB entry 1mru

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	8.5	277	1M Na citrate, 100mM CHES pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.39	48.64

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.987	α = 90
b = 52.099	β = 90
c = 143.371	γ = 90

Symmetry
Space Group	P 21 21 21

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	ADSC QUANTUM 210r		2003-06-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	1.1	ALS	8.3.1

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (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	1.9	15	96.3	0.048	10.4	3.2		25114

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
	1.9	2	99.2		0.321	2.7	3.3	3733

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 (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 1mru	1.9	15.28	23736	1276	100	0.21122	0.20861	0.22	0.25972	0.27	RANDOM	48.221

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]
3.66			-1.32		-2.34

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.22
r_dihedral_angle_4_deg	17.812
r_dihedral_angle_3_deg	14.991
r_dihedral_angle_1_deg	5.911
r_scangle_it	3.049
r_scbond_it	1.937
r_angle_refined_deg	1.566
r_mcangle_it	1.153
r_mcbond_it	0.843
r_angle_other_deg	0.826
r_symmetry_vdw_other	0.226
r_nbd_refined	0.217
r_nbd_other	0.181
r_nbtor_refined	0.176
r_mcbond_other	0.167
r_xyhbond_nbd_refined	0.16
r_symmetry_vdw_refined	0.115
r_chiral_restr	0.088
r_nbtor_other	0.087
r_symmetry_hbond_refined	0.045
r_bond_refined_d	0.014
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2060
Nucleic Acid Atoms
Solvent Atoms	71
Heterogen Atoms	43

Software

Software
Software Name	Purpose
Blu-Ice	data collection
EPMR	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling