1Z9W

Tetrameric structure of apo-7,8-Dihydroneopterin Aldolase from Mycobacterium tuberculosis

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1NBU	PDB ENTRY 1NBU

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7.6	300	PEG 4000, SODIUM ACETATE, PH 4.6, pH 7.60, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
1.73	29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 72.957	α = 90
b = 72.957	β = 90
c = 42.868	γ = 90

Symmetry
Space Group	I 4

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 4		2003-04-08	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X8C	0.9786	NSLS	X8C

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	100	99	0.078	31.3			3990		1

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	2.5	3	100		0.371	7.6

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 (All)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1NBU	2.5	51.57	3548	3548	393	98.75	0.18441	0.18441	0.17854	0.23429	RANDOM	37.451

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		1.86

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.585
r_dihedral_angle_4_deg	24.087
r_dihedral_angle_3_deg	16.679
r_dihedral_angle_1_deg	8.864
r_scangle_it	5.585
r_scbond_it	3.565
r_mcangle_it	2.475
r_angle_refined_deg	2.261
r_mcbond_it	1.363
r_nbtor_refined	0.315

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	41.585
r_dihedral_angle_4_deg	24.087
r_dihedral_angle_3_deg	16.679
r_dihedral_angle_1_deg	8.864
r_scangle_it	5.585
r_scbond_it	3.565
r_mcangle_it	2.475
r_angle_refined_deg	2.261
r_mcbond_it	1.363
r_nbtor_refined	0.315
r_nbd_refined	0.241
r_symmetry_vdw_refined	0.24
r_xyhbond_nbd_refined	0.194
r_chiral_restr	0.139
r_symmetry_hbond_refined	0.13
r_bond_refined_d	0.018
r_gen_planes_refined	0.01

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	821
Nucleic Acid Atoms
Solvent Atoms	25
Heterogen Atoms

Software

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

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.