3IQE

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methylene-tetrahydromethanopterin and coenzyme F420

X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	1QV9	PDB ENTRY 1QV9

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	6.5	291	30% PEG400, 0.1M MES, 0.1M sodium acetate, pH6.5, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K

Crystal Properties
Matthews coefficient	Solvent content
2.48	50.4

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 61.148	α = 90
b = 165.539	β = 99.14
c = 93.552	γ = 90

Symmetry
Space Group	P 1 21 1

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	MARMOSAIC 225 mm CCD		2007-09-05	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	0.9918	SLS	X10SA

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	1.8	92.5	95.7	0.074	15.6	3.4		169214		-3

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	1.8	1.9	94.9		0.411	2.8	2.6	11198

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Cut-off Sigma (I)	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	PDB ENTRY 1QV9	1.8	92.45	-0.3	153747	8157	95.68	0.19162	0.18974	0.22771	RANDOM	20.67

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]
-0.83		-1	0.78		-0.27

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.789
r_dihedral_angle_4_deg	17.78
r_dihedral_angle_3_deg	16.185
r_dihedral_angle_1_deg	5.75
r_scangle_it	3.854
r_scbond_it	2.407
r_angle_other_deg	2.342
r_angle_refined_deg	1.627
r_mcangle_it	1.384
r_mcbond_it	0.82

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.789
r_dihedral_angle_4_deg	17.78
r_dihedral_angle_3_deg	16.185
r_dihedral_angle_1_deg	5.75
r_scangle_it	3.854
r_scbond_it	2.407
r_angle_other_deg	2.342
r_angle_refined_deg	1.627
r_mcangle_it	1.384
r_mcbond_it	0.82
r_mcbond_other	0.243
r_chiral_restr	0.098
r_bond_refined_d	0.014
r_gen_planes_refined	0.008
r_bond_other_d
r_gen_planes_other

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	13092
Nucleic Acid Atoms
Solvent Atoms	634
Heterogen Atoms	457

Software

Software
Software Name	Purpose
AMoRE	phasing
REFMAC	refinement
XDS	data reduction
XDS	data scaling

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.