3IQF

Structure of F420 dependent methylene-tetrahydromethanopterin dehydrogenase in complex with methenyl-tetrahydromethanopterin

X-RAY DIFFRACTION

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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
2.57	52.18

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 103.4	α = 90
b = 167.1	β = 113.6
c = 122.5	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		2009-03-03	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	SLS BEAMLINE X10SA	1.008	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	2	112.5	99.2	0.062	14.9	4	256709	246709		-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	2	2.1	77.6		0.511	2.7	77.6	35779

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	2.1	112.5	-3	208672	11021	99.23	0.16246	0.16048	0.20028	RANDOM	26.099

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]
-0.96		-0.06	0.77		0.014

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	37.654
r_dihedral_angle_4_deg	16.253
r_dihedral_angle_3_deg	15.432
r_dihedral_angle_1_deg	7.128
r_scangle_it	4.34
r_scbond_it	2.65
r_angle_refined_deg	1.631
r_mcangle_it	1.355
r_angle_other_deg	0.949
r_mcbond_it	0.68
r_symmetry_metal_ion_refined	0.467
r_metal_ion_refined	0.447
r_symmetry_vdw_refined	0.406
r_symmetry_hbond_refined	0.308
r_mcbond_other	0.218
r_nbd_refined	0.216
r_symmetry_vdw_other	0.202
r_nbd_other	0.192
r_nbtor_refined	0.176
r_xyhbond_nbd_refined	0.169
r_chiral_restr	0.098
r_nbtor_other	0.089
r_xyhbond_nbd_other	0.079
r_bond_refined_d	0.017
r_gen_planes_refined	0.007
r_bond_other_d	0.002
r_gen_planes_other	0.002
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	26184
Nucleic Acid Atoms
Solvent Atoms	1068
Heterogen Atoms	548

Software

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