2O1C | pdb_00002o1c

Structure of the E. coli dihydroneopterin triphosphate pyrophosphohydrolase

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	6.8	298	1.3-1.5 Ammonium sulfate, 1% propanol, 3-5 mM DTT, 4mM sodium pyrophosphate, 100mM Na Hepes pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K

Crystal Properties
Matthews coefficient	Solvent content
1.84	32.99

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.104	α = 90
b = 42.579	β = 115.69
c = 106.467	γ = 90

Symmetry
Space Group	C 1 2 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	IMAGE PLATE	FUJI		1997-04-10	M	SINGLE WAVELENGTH
2	1	x-ray	298	IMAGE PLATE	RIGAKU RAXIS IIC		1998-08-08	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X4A	1.1	NSLS	X4A
2	ROTATING ANODE	RIGAKU RU200	1.541

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Sym 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	1.8	95.945	95.6	0.086	10.2			44935

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1,2	1.8	1.88	95.7		0.342

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	MIR	THROUGHOUT	1.8	95.78	44933	2238	95.62	0.229	0.226	0.2258	0.289	0.2857	RANDOM	21.949

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		0.64	-0.32		0.59

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.783
r_dihedral_angle_4_deg	16.88
r_dihedral_angle_3_deg	15.036
r_dihedral_angle_1_deg	5.736
r_scangle_it	2.132
r_scbond_it	1.411
r_angle_refined_deg	1.237
r_mcangle_it	0.838
r_mcbond_it	0.519
r_symmetry_vdw_refined	0.414
r_nbtor_refined	0.301
r_nbd_refined	0.206
r_symmetry_hbond_refined	0.151
r_xyhbond_nbd_refined	0.15
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.004

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4706
Nucleic Acid Atoms
Solvent Atoms	611
Heterogen Atoms	47

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction
SHARP	phasing