2VZZ | pdb_00002vzz

Crystal structure of Rv0802c from Mycobacterium tuberculosis in Complex with Succinyl-CoA

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2VZY	PDB ENTRY 2VZY

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7		PROTEIN AT 8 MG/ML IN 20 MM TEA PH 8.5, 100 MM AMMONIUM SULFATE, 1 MM EDTA, 1 MM DTT, 2 MM COA, 4 MM SUCCOA CRYSTALLIZED IN 1 M LICL, 100 MM HEPES PH 7.0. CRYOPROTECTED IN PRECIPITANT SOLUTION PLUS 20 MM SUCCOA AND 20% GLYCEROL

Crystal Properties
Matthews coefficient	Solvent content
3.03	54

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.165	α = 90
b = 135.172	β = 90
c = 164.077	γ = 90

Symmetry
Space Group	I 2 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	93	IMAGE PLATE	RIGAKU IMAGE PLATE	OSMIC BLUE CONFOCAL	2004-03-16	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU RUH3R

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	2.3	104	95.9	0.06	15.3	3.5		53759

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)
1	2.3	2.38	92.8		0.2	4.8	3

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 2VZY	2.3	104.26	51029	2730	95.8	0.172	0.169	0.17	0.222	0.22	RANDOM	19.81

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]
0.33			1.26		-1.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.199
r_dihedral_angle_4_deg	16.542
r_dihedral_angle_3_deg	14.568
r_dihedral_angle_1_deg	5.914
r_scangle_it	3.623
r_scbond_it	2.247
r_angle_refined_deg	1.684
r_mcangle_it	1.321
r_mcbond_it	0.779
r_nbtor_refined	0.304
r_nbd_refined	0.204
r_symmetry_vdw_refined	0.188
r_symmetry_hbond_refined	0.155
r_xyhbond_nbd_refined	0.141
r_chiral_restr	0.103
r_bond_refined_d	0.015
r_gen_planes_refined	0.006
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
r_nbd_other
r_nbtor_other
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_other
r_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6763
Nucleic Acid Atoms
Solvent Atoms	413
Heterogen Atoms	220

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
AMoRE	phasing