3H5H | pdb_00003h5h

LeuD_1-186 small subunit of isopropylmalate isomerase (Rv2987c) from mycobacterium tuberculosis

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	3H5E	PDB ENTRY 3H5E

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	7	293	0.1M NaCl, 0.1M Hepes pH 7.0, 1.2M Ammonium sulphate, VAPOR DIFFUSION, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
1.9	35.41

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 90.48	α = 90
b = 70.29	β = 124.05
c = 59.65	γ = 90

Symmetry
Space Group	C 1 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	MARMOSAIC 225 mm CCD		2008-12-11	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID23-2	0.873	ESRF	ID23-2

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	2.5	51	98.9	0.171	7.6	4.6	10727	10727	2	2	37.4

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)
	2.5	2.56	92.3		0.447	2.2	4.2

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 3H5E	2.5	30	10727	10185	518	99.04	0.22788	0.2257	0.22	0.26863	0.26	RANDOM	19

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]
-0.42		-1.22	-1.04		0.09

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.411
r_dihedral_angle_3_deg	17.95
r_dihedral_angle_4_deg	15.308
r_dihedral_angle_1_deg	5.076
r_scangle_it	4.059
r_scbond_it	2.398
r_mcangle_it	1.103
r_angle_refined_deg	1.074
r_mcbond_it	0.553
r_chiral_restr	0.07
r_bond_refined_d	0.007
r_gen_planes_refined	0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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
r_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2593
Nucleic Acid Atoms
Solvent Atoms	39
Heterogen Atoms

Software

Software
Software Name	Purpose
DNA	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALEPACK	data scaling