2DEG | pdb_00002deg

Crystal structure of tt0972 protein form Thermus Thermophilus with Mn2(+) ions

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	2CZ8	PDB ENTRY 2CZ8

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	5.6	293	30% MPD, 200mM ammonium acetate, 100mM lithium chloride, 10mM manganese chloride, 100mM citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.32	46.95

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 65.324	α = 90
b = 65.324	β = 90
c = 202.366	γ = 90

Symmetry
Space Group	P 41 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	IMAGE PLATE	RIGAKU RAXIS V	mirrors	2005-04-19	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SPRING-8 BEAMLINE BL26B2	1.0	SPring-8	BL26B2

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	1.7	30	99.8	0.044	33.1	4.8	49401	49302		-3	27.1

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	1.7	1.75	100		0.399	4	5	4026

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	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 2CZ8	1.7	10	46428	46428	2478	99.81	0.24	0.23845	0.23629	0.2354	0.2787	0.2794	RANDOM	33.97

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]
0.45			0.45		-0.9

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	27.633
r_dihedral_angle_4_deg	18.991
r_dihedral_angle_3_deg	13.55
r_dihedral_angle_1_deg	5.652
r_scangle_it	5.164
r_scbond_it	3.089
r_mcangle_it	1.946
r_angle_refined_deg	1.542
r_mcbond_it	1.087
r_nbtor_refined	0.31
r_nbd_refined	0.205
r_metal_ion_refined	0.189
r_symmetry_vdw_refined	0.153
r_symmetry_hbond_refined	0.133
r_xyhbond_nbd_refined	0.129
r_chiral_restr	0.099
r_bond_refined_d	0.015
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3185
Nucleic Acid Atoms
Solvent Atoms	182
Heterogen Atoms	15

Software

Software
Software Name	Purpose
REFMAC	refinement
BSS	data collection
SCALEPACK	data scaling
AMoRE	phasing