1VMJ

CRYSTAL STRUCTURE OF A PUTATIVE THIAMIN PHOSPHATE SYNTHASE (TM0723) FROM THERMOTOGA MARITIMA MSB8 AT 1.52 A RESOLUTION

X-RAY DIFFRACTION

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Starting Model(s)

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

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION,SITTING DROP,NANODROP	6	293	3.2M (NH4)2SO4, 0.1M MES pH 6.0, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

Crystal Properties
Matthews coefficient	Solvent content
2.85	56.48

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 110.194	α = 90
b = 110.194	β = 90
c = 110.194	γ = 90

Symmetry
Space Group	P 43 3 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	flat mirror	2001-12-09	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	1.52	27.55	100	0.115	19.2	20.5		35764			24.03

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	1.52	1.6	100		0.01166	2	8.8	5117

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	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	THROUGHOUT	1VMF	1.52	27.55	33973	1790	99.94	0.14495	0.144	0.16302	RANDOM	15.684

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]

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	38.858
r_dihedral_angle_4_deg	13.907
r_dihedral_angle_3_deg	11.836
r_dihedral_angle_1_deg	6.717
r_scangle_it	5.35
r_scbond_it	3.674
r_mcangle_it	2.277
r_mcbond_it	1.402
r_angle_refined_deg	1.358
r_angle_other_deg	0.795
r_mcbond_other	0.411
r_symmetry_vdw_other	0.284
r_metal_ion_refined	0.266
r_nbd_refined	0.24
r_nbd_other	0.196
r_nbtor_refined	0.179
r_xyhbond_nbd_refined	0.166
r_symmetry_hbond_refined	0.144
r_symmetry_vdw_refined	0.128
r_chiral_restr	0.084
r_nbtor_other	0.084
r_bond_refined_d	0.011
r_gen_planes_refined	0.006
r_bond_other_d	0.002
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	1138
Nucleic Acid Atoms
Solvent Atoms	213
Heterogen Atoms	16

Software

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