1ZUP | pdb_00001zup

CRYSTAL STRUCTURE OF A PUTATIVE NUCLEASE WITH A RIBONUCLEASE H-LIKE MOTIF FOLD (TM1739) FROM THERMOTOGA MARITIMA AT 2.20 A RESOLUTION

X-RAY DIFFRACTION

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Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP, NANODROP		277	0.10M Acetate_Na, 0.03M HCl, 8.00% MPD, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K
2	VAPOR DIFFUSION, SITTING DROP, NANODROP		277	0.10M Acetate_Na, 0.03M HCl, 7.00% MPD, VAPOR DIFFUSION, SITTING DROP, NANODROP, temperature 277K

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 82.433	α = 90
b = 82.433	β = 90
c = 234.492	γ = 90

Symmetry
Space Group	P 43 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	Double crystal Si(111)	2003-12-20	M	SINGLE WAVELENGTH
2	1	x-ray	100	CCD	ADSC QUANTUM 210	Double crystal Si(111)	2004-01-08	M	SINGLE WAVELENGTH
1,2	1

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ALS BEAMLINE 8.2.2	1.0000	ALS	8.2.2
2	SYNCHROTRON	ALS BEAMLINE 8.2.1	0.9794	ALS	8.2.1

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
1,2	2.1	41.22	100	0.121	5.5	9.2		48259

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	2.1	2.15	100		0.01375	0.01375	1.6	6.8

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-Factor (Observed)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	SAD	THROUGHOUT	2.2	20	39863	2114	99.93	0.23	0.22988	0.228	0.24	0.266	0.27	RANDOM	60.792

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]
0.42			0.42		-0.84

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.672
r_dihedral_angle_3_deg	16.522
r_dihedral_angle_4_deg	15.978
r_scangle_it	8.85
r_dihedral_angle_1_deg	7.084
r_scbond_it	6.255
r_mcangle_it	3.511
r_mcbond_it	2.422
r_angle_refined_deg	1.651
r_angle_other_deg	0.826
r_mcbond_other	0.653
r_symmetry_vdw_refined	0.345
r_symmetry_vdw_other	0.303
r_nbd_refined	0.213
r_nbtor_refined	0.187
r_nbd_other	0.179
r_symmetry_hbond_refined	0.169
r_xyhbond_nbd_refined	0.16
r_chiral_restr	0.09
r_nbtor_other	0.088
r_xyhbond_nbd_other	0.04
r_bond_refined_d	0.018
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.002

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4349
Nucleic Acid Atoms
Solvent Atoms	70
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
MOSFLM	data reduction
CCP4	data scaling
SHARP	phasing