1TWL

Inorganic pyrophosphatase from Pyrococcus furiosus Pfu-264096-001

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1		8.6	291	1.5M K2HPO4, 0.1M TRIS-HCL, pH 8.6, modified microbatch, temperature 291K

Crystal Properties
Matthews coefficient	Solvent content
2.08	40.73

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 113.434	α = 90
b = 113.434	β = 90
c = 73.313	γ = 120

Symmetry
Space Group	H 3 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	MARMOSAIC 225 mm CCD		2004-06-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 22-ID	1.000	APS	22-ID

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	2.2	30	100	0.082				9314

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	2.2	2.28	99.7		0.381

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 (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	MOLECULAR REPLACEMENT	THROUGHOUT	PDB ENTRY 1UDE	2.201	29.361	9313	447	99.903	0.197	0.19657	0.1936	0.2	0.2574	0.26	RANDOM	28.67

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]
-0.024	-0.012		-0.024		0.036

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.515
r_dihedral_angle_4_deg	19.23
r_dihedral_angle_3_deg	13.961
r_dihedral_angle_1_deg	6.324
r_mcangle_it	3.435
r_scangle_it	3.157
r_mcbond_it	2.368
r_scbond_it	2.142
r_mcangle_other	1.98
r_scangle_other	1.432
r_angle_refined_deg	1.311
r_angle_other_deg	0.795
r_scbond_other	0.735
r_mcbond_other	0.575
r_symmetry_vdw_other	0.24
r_nbd_refined	0.191
r_nbtor_refined	0.184
r_symmetry_vdw_refined	0.184
r_nbd_other	0.176
r_symmetry_hbond_refined	0.149
r_xyhbond_nbd_refined	0.13
r_nbtor_other	0.083
r_chiral_restr	0.079
r_bond_refined_d	0.016
r_gen_planes_refined	0.005
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1370
Nucleic Acid Atoms
Solvent Atoms	35
Heterogen Atoms

Software

Software
Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
EPMR	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection