2O2I | pdb_00002o2i

Crystal structure of haloalkane dehalogenase Rv2579 from Mycobacterium tuberculosis complexed with 1,3-propandiol

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1MJ5	pdb entry 1MJ5

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	298	30% PEG 4000, 0.2M magnesium acetate, 0.1M Tris, 5% ethylene glycol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.85	33.5

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.82	α = 90
b = 65.19	β = 90
c = 126.09	γ = 90

Symmetry
Space Group	C 2 2 21

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray		CCD	ADSC QUANTUM 210		2006-05-11	M	SINGLE WAVELENGTH
2	1

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

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	1.5	63.043	98.4	0.097	5.2	4.3	40063	39855			10.1

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.5	1.58	92.9		0.193	0.193	3.6	2.8	5410

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	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 1MJ5	1.5	36.35	39807	39807	2003	98.29	0.146	0.144	0.15	0.176	0.18	RANDOM	9.054

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.484
r_dihedral_angle_4_deg	20.709
r_dihedral_angle_3_deg	12.144
r_dihedral_angle_1_deg	6.266
r_scangle_it	3.591
r_scbond_it	2.445
r_angle_refined_deg	1.843
r_mcangle_it	1.725
r_mcbond_it	1.336
r_angle_other_deg	1.086
r_symmetry_vdw_other	0.378
r_mcbond_other	0.376
r_nbd_refined	0.232
r_symmetry_hbond_refined	0.228
r_nbd_other	0.216
r_nbtor_refined	0.19
r_xyhbond_nbd_refined	0.146
r_chiral_restr	0.136
r_symmetry_vdw_refined	0.133
r_nbtor_other	0.09
r_bond_refined_d	0.021
r_gen_planes_refined	0.011
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2312
Nucleic Acid Atoms
Solvent Atoms	297
Heterogen Atoms	6

Software

Software
Software Name	Purpose
SCALA	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
ADSC	data collection
MOSFLM	data reduction