6TLK

Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1LU9 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP7.5281.15The protein at 25 mg/ml was in 25 mM tris(hydroxymethyl)aminomethane (Tris)/HCl buffer pH 7.5 containing 150 mM NaCl, 5% glycerol and 2 mM dithiothreitol, supplemented with 2.5 mM methenyl-H4MPT and 2 mM NADP. The crystallization solution was 20% w/v polyethylene glycol 3350 and 200 mM magnesium formate. The crystallization drop contained 0.7 ul of protein solution and 0.7 ul crystallization solution
Crystal Properties
Matthews coefficientSolvent content
2.5251.14

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 76.923α = 90
b = 149.267β = 93.64
c = 78.559γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC QUANTUM 315r2017-09-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE BM30A0.97992ESRFBM30A

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge I (Observed)R Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.878.40198.90.0660.0660.080.0440.9912.2316118928.48
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)R-Sym I (Observed)Rrim I (All)Rpim I (All)CC (Half)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.81.999.51.0321.0321.2470.690.5430.83

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT1LU91.826.35161135790998.80.1670.1660.201RANDOM36.17
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]
1.07545.0536-0.6214-0.454
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion13.72
t_omega_torsion3.63
t_angle_deg1.21
t_bond_d0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
RMS Deviations
KeyRefinement Restraint Deviation
t_other_torsion13.72
t_omega_torsion3.63
t_angle_deg1.21
t_bond_d0.009
t_dihedral_angle_d
t_trig_c_planes
t_gen_planes
t_it
t_nbd
t_improper_torsion
t_pseud_angle
t_chiral_improper_torsion
t_sum_occupancies
t_utility_distance
t_utility_angle
t_utility_torsion
t_ideal_dist_contact
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms12548
Nucleic Acid Atoms
Solvent Atoms2093
Heterogen Atoms489

Software

Software
Software NamePurpose
BUSTERrefinement
XDSdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
MOLREPphasing