2PTF

Crystal structure of protein MTH_863 from Methanobacterium thermoautotrophicum bound to FMN

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION	8.5	294	100 mM Tris-HCl, 50% MPD, 100 mM Ammonium phosphate, pH 8.5, VAPOR DIFFUSION, temperature 294K

Crystal Properties
Matthews coefficient	Solvent content
2.35	47.56

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 91.727	α = 90
b = 91.727	β = 90
c = 117.868	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	CCD	ADSC QUANTUM 315		2007-05-04	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	NSLS BEAMLINE X29A	0.9791	NSLS	X29A

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (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	2.35	45.883	99.9	0.087	0.087	26	12.5	21594	21594			38.6

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	2.35	2.48	100		0.413	0.413	5.9	12.8	3096

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (All)	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	SAD	THROUGHOUT	2.35	20	21546	21546	1092	100	0.201	0.199	0.253	RANDOM	41.36

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]
-1.1			-1.1		2.2

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.876
r_dihedral_angle_4_deg	18.933
r_dihedral_angle_3_deg	16.565
r_dihedral_angle_1_deg	6.593
r_scangle_it	5.105
r_scbond_it	3.182
r_mcangle_it	1.944
r_angle_refined_deg	1.568
r_mcbond_it	1.175
r_nbtor_refined	0.303

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	32.876
r_dihedral_angle_4_deg	18.933
r_dihedral_angle_3_deg	16.565
r_dihedral_angle_1_deg	6.593
r_scangle_it	5.105
r_scbond_it	3.182
r_mcangle_it	1.944
r_angle_refined_deg	1.568
r_mcbond_it	1.175
r_nbtor_refined	0.303
r_nbd_refined	0.206
r_symmetry_vdw_refined	0.2
r_xyhbond_nbd_refined	0.175
r_symmetry_hbond_refined	0.138
r_chiral_restr	0.103
r_bond_refined_d	0.018
r_gen_planes_refined	0.006

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	3189
Nucleic Acid Atoms
Solvent Atoms	118
Heterogen Atoms	62

Software

Software
Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
CBASS	data collection
DENZO	data reduction
CCP4	data scaling
SHELXCD	phasing
SHELXD	phasing
SHELXE	model building

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.