1NBU | pdb_00001nbu

7,8-Dihydroneopterin Aldolase Complexed with Product From Mycobacterium Tuberculosis

X-RAY DIFFRACTION

Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	4.6	300	PEG 4000, sodium acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 300K

Crystal Properties
Matthews coefficient	Solvent content
1.73	29

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 78.56	α = 90
b = 85.15	β = 112.69
c = 74.79	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	200	IMAGE PLATE	RIGAKU RAXIS IV	mirrors	2002-01-17	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	ROTATING ANODE	RIGAKU	1.5418

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	1.6	90	99.2	0.068			118185	118185	1	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)
	1.6	1.66	93.9		0.464

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 (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	AB INITIO	FREE R	PDB ENTRY 1DHN	1.6	10	111758	109918	4817	93.8	0.177	0.177	0.166	0.21	0.257	0.25	RANDOM

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]

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
		7947.25

RMS Deviations
Key	Refinement Restraint Deviation
s_anti_bump_dis_restr	0.1
s_approx_iso_adps	0.07
s_similar_adp_cmpnt	0.059
s_non_zero_chiral_vol	0.047
s_zero_chiral_vol	0.036
s_angle_d	0.029
s_from_restr_planes	0.0263
s_bond_d	0.019
s_rigid_bond_adp_cmpnt	0.002
s_similar_dist

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	7406
Nucleic Acid Atoms
Solvent Atoms	470
Heterogen Atoms	112

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
GLRF	phasing
SHELXL-97	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.