2GB5 | pdb_00002gb5

Crystal structure of NADH pyrophosphatase (EC 3.6.1.22) (1790429) from Escherichia coli K12 at 2.30 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP		277	9.975% PEG MME 5000, 0.05M Acetic Acid, 0.052M Citrate_Na3, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.36	47.44

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 99.287	α = 90
b = 103.553	β = 90
c = 57.27	γ = 90

Symmetry
Space Group	P 21 21 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 315		2003-10-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	0.9802, 1.0000	ALS	8.2.2

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.3	49.629	99.1	0.076	0.076	5.7	3.4		26695

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	R-Sym I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.3	2.36	91.6		0.384	0.384	2	2.7

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 (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	2.3	49.61	26666	1345	98.98	0.201	0.198	0.2	0.252	0.26	RANDOM	37.389

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]
-3.03			2.14		0.89

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.11
r_dihedral_angle_4_deg	17.118
r_dihedral_angle_3_deg	14.455
r_dihedral_angle_1_deg	6.225
r_scangle_it	5.296
r_scbond_it	3.819
r_mcangle_it	2.081
r_mcbond_it	1.599
r_angle_refined_deg	1.225
r_angle_other_deg	0.768
r_mcbond_other	0.377
r_nbd_other	0.175
r_nbtor_refined	0.171
r_nbd_refined	0.17
r_xyhbond_nbd_refined	0.165
r_symmetry_vdw_other	0.154
r_symmetry_hbond_refined	0.152
r_symmetry_vdw_refined	0.111
r_nbtor_other	0.082
r_chiral_restr	0.069
r_bond_refined_d	0.012
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4171
Nucleic Acid Atoms
Solvent Atoms	240
Heterogen Atoms	2

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
MOSFLM	data reduction
CCP4	data scaling
SOLVE	phasing