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Structure of methylene-tetrahydromethanopterin dehydrogenase from Methylorubrum extorquens AM1 in an open conformation containing NADP+ and methylene-H4MPT
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1LU9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 281.15 The 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 coefficient Solvent content 2.52 51.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 76.923 α = 90 b = 149.267 β = 93.64 c = 78.559 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 ADSC QUANTUM 315r 2017-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.97992 ESRF BM30A
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) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.8 78.401 98.9 0.066 0.066 0.08 0.044 0.99 12.2 3 161189 28.48
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) Redundancy Number Unique Reflections (All) 1 1.8 1.9 99.5 1.032 1.032 1.247 0.69 0.543 0.8 3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1LU9 1.8 26.35 161135 7909 98.8 0.167 0.166 0.201 0.1878 RANDOM 36.17
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] 1.0754 5.0536 -0.6214 -0.454
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.72 t_omega_torsion 3.63 t_angle_deg 1.21 t_bond_d 0.009 t_dihedral_angle_d t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.72 t_omega_torsion 3.63 t_angle_deg 1.21 t_bond_d 0.009 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 Atoms Number Protein Atoms 12548 Nucleic Acid Atoms Solvent Atoms 2093 Heterogen Atoms 489
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling PDB_EXTRACT data extraction MOLREP phasing