2NM2

Crystal structure of dihydroneopterin aldolase from S. aureus in complex with (1S,2R)-neopterin at 1.50 Angstrom resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2NM3	PDB ENTRY 2NM3

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		7.5	292	0.8M Sodium-potassium tartrate, 0.1M HEPES, 10mM Tris-HCL, pH 7.50, VAPOR DIFFUSION, HANGING DROP, temperature 292K

Crystal Properties
Matthews coefficient	Solvent content
2.01	38.9

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 60.033	α = 90
b = 60.033	β = 90
c = 123.057	γ = 90

Symmetry
Space Group	P 42

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	2003-08-05	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	1.7	30	92.1	0.053	18.5	3.8		43915			18.2

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	1.7	1.76	88.3		0.359	1.98	2.2

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 2NM3	1.7	22.46	42055	2047	88	0.22	0.22	0.262	RANDOM	26.8

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]
1.09			1.09		-2.18

Coordinate Error
Structure Solution Method	Refinement High Resolution	Refinement Low Resolution
		4685

RMS Deviations
Key	Refinement Restraint Deviation
c_dihedral_angle_d	23.9
c_scangle_it	3.95
c_scbond_it	2.64
c_mcangle_it	2.14
c_angle_deg	1.4
c_mcbond_it	1.4
c_improper_angle_d	0.76
c_bond_d	0.007
c_bond_d_na
c_bond_d_prot
c_angle_d
c_angle_d_na
c_angle_d_prot
c_angle_deg_na
c_angle_deg_prot
c_dihedral_angle_d_na
c_dihedral_angle_d_prot
c_improper_angle_d_na
c_improper_angle_d_prot

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3868
Nucleic Acid Atoms
Solvent Atoms	642
Heterogen Atoms	72

Software

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