4IHI | pdb_00004ihi

Crystal structure of the Delta-pyrroline-5-carboxylate dehydrogenase from Mycobacterium tuberculosis bound with NAD

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.1	291	0.1 M Bicine/Tris pH 8.1, 12% polyethylene glycol (PEG) 1000, 12% PEG 3350, 12% 2-methyl-2,4-pentandiol (MPD), 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate and 0.03 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
6.25	80.31

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 163.937	α = 90
b = 163.937	β = 90
c = 194.025	γ = 120

Symmetry
Space Group	P 6 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	100	CCD	ADSC QUANTUM 315r		2011-07-22	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	AUSTRALIAN SYNCHROTRON BEAMLINE MX2	0.953688	Australian Synchrotron	MX2

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	1.91	29.65	99.8				73091

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	1.91	2.02	98.6

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	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	2.25	29.51	68453	3641	98.46	0.27665	0.27503	0.28	0.30723	0.31	RANDOM	15.087

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]
-0.29	-0.14		-0.29		0.43

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.954
r_dihedral_angle_4_deg	21.872
r_dihedral_angle_3_deg	14.344
r_dihedral_angle_1_deg	6.778
r_angle_refined_deg	1.928
r_angle_other_deg	1.069
r_chiral_restr	0.12
r_bond_refined_d	0.02
r_gen_planes_refined	0.01
r_bond_other_d	0.001
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
r_mcbond_it
r_mcbond_other
r_mcangle_it
r_scbond_it
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4098
Nucleic Acid Atoms
Solvent Atoms	450
Heterogen Atoms	44

Software

Software
Software Name	Purpose
Blu-Ice	data collection
MOLREP	phasing
REFMAC	refinement
XDS	data reduction
SCALA	data scaling