1VJ2

Crystal structure of a novel family of manganese-containing cupin (tm1459) from thermotoga maritima at 1.65 A resolution

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1FI2

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	5.2	293	50% (v/v) PEG-200, 0.1M Phosphate-citrate pH 4.2 0.2M NaCl, pH 5.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.71	54.2

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 52.55	α = 90
b = 52.55	β = 90
c = 96.267	γ = 120

Symmetry
Space Group	P 32

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	flat mirror	2002-01-09	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SSRL BEAMLINE BL11-1		SSRL	BL11-1

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	1.65	48.13	97.8	0.057	15.6	3.6	35029	35029			30.49

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)
	1.65	1.74	87.6		0.466	1.9	2.7	4592

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 (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	1FI2	1.65	33.07	33262	1729	97.78	0.21015	0.20817	0.2	0.24859	0.2	RANDOM	24.615

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]
0.98	0.49		0.98		-1.47

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.829
r_dihedral_angle_4_deg	23.596
r_dihedral_angle_3_deg	18.157
r_dihedral_angle_1_deg	6.971
r_scangle_it	3.338
r_scbond_it	2.509
r_angle_refined_deg	1.652
r_mcangle_it	1.351
r_mcbond_it	1.179
r_angle_other_deg	0.854
r_symmetry_vdw_other	0.272
r_nbd_other	0.193
r_nbd_refined	0.186
r_symmetry_hbond_refined	0.151
r_symmetry_vdw_refined	0.137
r_chiral_restr	0.103
r_nbtor_other	0.091
r_xyhbond_nbd_refined	0.054
r_bond_refined_d	0.018
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1850
Nucleic Acid Atoms
Solvent Atoms	169
Heterogen Atoms	6

Software

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