1U6K | pdb_00001u6k

TLS refinement of the structure of Se-methionine labelled Coenzyme f420-dependent methylenetetrahydromethanopterin dehydrogenase (MTD) from Methanopyrus kandleri

X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	7	277	MOPS, KOH, MPD, PEG 400, Mg acetate, Na phosphate, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

Crystal Properties
Matthews coefficient	Solvent content
2.6	48.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 120.1	α = 90
b = 151.2	β = 90
c = 110	γ = 90

Symmetry
Space Group	C 2 2 21

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 4		2002-07-11	M	MAD

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	ESRF BEAMLINE ID14-4	0.9792, 0.9797, 0.95	ESRF	ID14-4

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	1.54	20	99.1	0.075	17.7	3.5		145808			21.4

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	1.54	1.62	99.9		0.257	3.9	3.5	15700

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-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	MAD	THROUGHOUT	1.55	20	135825	135825	7207	99.1	0.17829	0.18	0.19546	0.19	RANDOM	13.914

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]
2.48			-1.72		-0.76

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	3.733
r_scbond_it	2.352
r_dihedral_angle_1_deg	2.098
r_angle_refined_deg	1.778
r_mcangle_it	1.148
r_mcbond_it	0.588
r_symmetry_vdw_refined	0.291
r_nbd_refined	0.236
r_symmetry_hbond_refined	0.172
r_xyhbond_nbd_refined	0.148

RMS Deviations
Key	Refinement Restraint Deviation
r_scangle_it	3.733
r_scbond_it	2.352
r_dihedral_angle_1_deg	2.098
r_angle_refined_deg	1.778
r_mcangle_it	1.148
r_mcbond_it	0.588
r_symmetry_vdw_refined	0.291
r_nbd_refined	0.236
r_symmetry_hbond_refined	0.172
r_xyhbond_nbd_refined	0.148
r_chiral_restr	0.133
r_metal_ion_refined	0.07
r_bond_refined_d	0.014
r_gen_planes_refined	0.009

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	6546
Nucleic Acid Atoms
Solvent Atoms	580
Heterogen Atoms	4

Software

Software
Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
SCALEPACK	data scaling
SHELXD	phasing
SHARP	phasing

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 R01GM157729.