1VMG | pdb_00001vmg

Crystal structure of MazG nucleotide pyrophosphohydrolase (13816655) from Sulfolobus solfataricus at 1.46 A resolution

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	7.5	277	1.5M Li2SO4, 0.1M HEPES pH 7.5, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
3.3	62.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 79.749	α = 90
b = 79.749	β = 90
c = 95.909	γ = 90

Symmetry
Space Group	I 41 2 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		2004-09-18	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.3.1	0.979834,0.979694,1.020035	ALS	8.3.1

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	1.46	25.62	93.3	0.044	19.6	5.9		25360			23.08

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	1.46	1.54	57.6		0.435	2.2	2	2241

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	MAD	THROUGHOUT	1.46	25.62	24059	1288	93.34	0.14201	0.14178	0.15	0.14633	0.16	RANDOM	14.062

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]
-0.19			-0.19		0.38

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	35.014
r_dihedral_angle_4_deg	14.745
r_dihedral_angle_3_deg	12.092
r_scangle_it	5.367
r_dihedral_angle_1_deg	4.933
r_scbond_it	4.279
r_mcangle_it	2.371
r_mcbond_it	1.903
r_angle_refined_deg	1.235
r_angle_other_deg	0.8
r_xyhbond_nbd_refined	0.381
r_mcbond_other	0.318
r_nbd_refined	0.253
r_metal_ion_refined	0.204
r_nbtor_refined	0.183
r_symmetry_hbond_refined	0.177
r_nbd_other	0.149
r_symmetry_vdw_other	0.133
r_symmetry_vdw_refined	0.115
r_nbtor_other	0.084
r_chiral_restr	0.076
r_bond_refined_d	0.012
r_gen_planes_refined	0.005
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	655
Nucleic Acid Atoms
Solvent Atoms	106
Heterogen Atoms	10

Software

Software
Software Name	Purpose
XDS	data scaling
SCALA	data scaling
SHELX	model building
autoSHARP	phasing
REFMAC	refinement
XDS	data reduction
CCP4	data scaling
SHELX	phasing