2C82 | pdb_00002c82

X-Ray Structure Of 1-Deoxy-D-xylulose 5-phosphate Reductoisomerase, DXR, Rv2870c, 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	1Q0Q	PDB ENTRY 1Q0Q

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP			THE SITTING DROPS CONTAINED 1 ML PROTEIN, 5.35 MG/ML, WITH A FINAL CONCENTRATION OF 0.64 MM OF FOSMIDOMYCIN, DISSOLVED IN 10 MM TRIS PH 8.0, AND 1 ML CRYSTALLIZATION BUFFER (40% ETHYLENE GLYCOL, 2 MM MGSO4, 20 MM DTT, 0.2 MM EDTA, AND 100 MM ACETATE PH 5.0). THE RESERVOIR SOLUTION CONSISTED OF A MIXTURE BETWEEN THE CRYSTALLIZATION BUFFER, AND THE BUFFER USED IN THE FINAL STEPS OF THE PROTEIN PURIFICATION (75 MM NACL, 10 MM TRIS-HCL PH 7.5, 20% ETHYLENE GLYCOL, 1 MM MGSO4, 10 MM DTT, 0.1 MM EDTA, AND 50 MM ACETATE PH 5.0). BEFORE THE CRYSTALS WERE FLASH-COOLED IN LIQUID NITROGEN THEY WERE TRANSFERRED TO A DROP WITH THE RESERVOIR SOLUTION COMPLEMENTED WITH AN ADDITIONAL 10% ETHYLENE GLYCOL, AND 1 MM FOSMIDOMYCIN.

Crystal Properties
Matthews coefficient	Solvent content
2.3	46

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 56.931	α = 90
b = 56.931	β = 90
c = 238.997	γ = 90

Symmetry
Space Group	P 41

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	110	CCD	MARRESEARCH		2005-07-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-1		ESRF	ID14-1

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	1.9	40	99.7	0.08	6.2	3.4		56321

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	1.9	1.95	99.8		0.39

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 1Q0Q	1.9	40	56321	2962	99.7	0.216	0.215	0.21	0.247	0.25	RANDOM	35.13

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]
0.93			0.93		-1.87

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.689
r_dihedral_angle_4_deg	19.42
r_dihedral_angle_3_deg	12.982
r_dihedral_angle_1_deg	4.949
r_scangle_it	3.004
r_scbond_it	1.838
r_mcangle_it	1.3
r_angle_refined_deg	1.148
r_mcbond_it	0.794
r_nbtor_refined	0.296
r_symmetry_vdw_refined	0.201
r_nbd_refined	0.196
r_xyhbond_nbd_refined	0.132
r_symmetry_hbond_refined	0.132
r_chiral_restr	0.078
r_bond_refined_d	0.009
r_gen_planes_refined	0.004
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	5562
Nucleic Acid Atoms
Solvent Atoms	334
Heterogen Atoms	10

Software

Software
Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PHASER	phasing