2O5W | pdb_00002o5w

Structure of the E. coli dihydroneopterin triphosphate pyrophosphohydrolase in complex with Sm+3 and pyrophosphate

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
1.89	34.81

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 124.416	α = 90
b = 42.909	β = 115.19
c = 108.328	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	298	IMAGE PLATE	RIGAKU RAXIS IIC		1998-04-01	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	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	2.6	19.97	99.6	0.096				14304

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)
	2.6	2.67	98.9		0.326

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	2.6	19.97	13574	729	87.66	0.2	0.195	0.195	0.287	0.282	RANDOM	35.097

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]
0.46		1.72	-1.97		2.97

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	34.508
r_dihedral_angle_3_deg	18.212
r_dihedral_angle_4_deg	15.843
r_dihedral_angle_1_deg	5.831
r_scangle_it	1.709
r_scbond_it	1.697
r_angle_refined_deg	1.152
r_mcangle_it	0.796
r_mcbond_it	0.416
r_nbtor_refined	0.304
r_symmetry_vdw_refined	0.21
r_nbd_refined	0.209
r_xyhbond_nbd_refined	0.167
r_symmetry_hbond_refined	0.153
r_chiral_restr	0.079
r_bond_refined_d	0.009
r_gen_planes_refined	0.003

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4706
Nucleic Acid Atoms
Solvent Atoms	69
Heterogen Atoms	43

Software

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