2NM3

Crystal structure of dihydroneopterin aldolase from S. aureus in complex with (1S,2S)-monapterin at 1.68 angstrom resolution

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		6.5	292	1.4M Sodium acetate, 0.2M Imidazole, 0.1M Sodium cacodylate, 10mM Tris-HCL, pH 6.50, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.12	41.87

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.191	α = 90
b = 61.191	β = 90
c = 124.528	γ = 90

Symmetry
Space Group	I 4 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 4	MIRROR	2004-04-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X9B		NSLS	X9B

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	1.68	30	98	0.058	31.32	10.472		13718

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	1.68	1.74	88.7		0.388	2.09	9.31

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (F)	Number Reflections (All)	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	FREE R	PDB ENTRY 1DHN	1.68	30	4	12928	720	92.9	0.227	0.224		0.262	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
3		1156.5

RMS Deviations
Key	Refinement Restraint Deviation
s_similar_adp_cmpnt	0.087
s_anti_bump_dis_restr	0.076
s_zero_chiral_vol	0.054
s_non_zero_chiral_vol	0.044
s_angle_d	0.023
s_from_restr_planes	0.023
s_bond_d	0.007
s_similar_dist
s_rigid_bond_adp_cmpnt
s_approx_iso_adps

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	967
Nucleic Acid Atoms
Solvent Atoms	172
Heterogen Atoms	22

Software

Software
Software Name	Purpose
AMoRE	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

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.