4KL7 | pdb_00004kl7

Crystal structure of the catalytic domain of RpfB from Mycobacterium tuberculosis

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.5	293	6 mg mL-1, 0,5% (w/v) PEG8000, 1M ammonium sulphate, 0,1 M Hepes, pH 7.5, and 120 mM benzamidine , VAPOR DIFFUSION, HANGING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.07	40.61

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 42.427	α = 90
b = 51.595	β = 104.06
c = 66.594	γ = 90

Symmetry
Space Group	P 1 21 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	Saturn944			M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU MICROMAX-007	1.5

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	1.45	30	92.6			38135	38135

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	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	1.45	25.327	2076	82.21	0.14727	0.14487	0.15	0.19221	0.2	RANDOM	14.104

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]
-0.32		-0.39	1.16		-1.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.801
r_dihedral_angle_4_deg	16.881
r_dihedral_angle_3_deg	13.487
r_dihedral_angle_1_deg	6.78
r_sphericity_free	5.693
r_scangle_it	4.387
r_scbond_it	3.054
r_sphericity_bonded	2.216
r_mcangle_it	2.094
r_angle_refined_deg	1.531
r_rigid_bond_restr	1.493
r_mcbond_it	1.36
r_angle_other_deg	1.088
r_mcbond_other	0.546
r_chiral_restr	0.108
r_bond_refined_d	0.016
r_gen_planes_refined	0.008
r_bond_other_d	0.002
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2392
Nucleic Acid Atoms
Solvent Atoms	516
Heterogen Atoms	10

Software

Software
Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling