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Asymmetric [Fe]-hydrogenase from Methanolacinia paynteri apo and in complex with FeGP at 2.1-A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4JJF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 283.15 [Fe]-hydrogenase holoenzyme from M. paynteri was crystallized under 95%N2/5%H2 using 96-well two-drop MRC crystallization plates (sitting drop vapor diffusion method). 0.7 ul of 25-mg/ml reconstituted holoenzyme was mixed with 0.7-ul reservoir solution under yellow light and incubated under dark conditions. The crystals grew within two weeks in 30% w/v polyethylene glycol 4000, 200-mM lithium sulfate and 100-mM Tris pH 8.5 (JBScreen Wizard 3&4 HTS, Jena Bioscience).
Crystal Properties Matthews coefficient Solvent content 2.1 41.45
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 79.481 α = 90 b = 79.481 β = 90 c = 179.337 γ = 120
Symmetry Space Group P 31 2 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 2016-09-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE BM30A 0.97980 ESRF BM30A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 2.1 68.833 100 0.059 0.062 0.019 1 28.8 10.8 39181 41.7
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 2.1 2.21 100 0.711 0.711 0.746 0.222 0.755 1.1 11.1
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 4JJF 2.1 39.74 39126 1876 99.9 0.197 0.195 0.2029 0.235 0.2459 RANDOM 61.86
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] -0.4312 -0.4312 0.8623
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.57 t_omega_torsion 1.66 t_angle_deg 1.01 t_bond_d 0.008 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 14.57 t_omega_torsion 1.66 t_angle_deg 1.01 t_bond_d 0.008 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 5196 Nucleic Acid Atoms Solvent Atoms 224 Heterogen Atoms 103
Software Software Software Name Purpose SCALA data scaling BUSTER refinement PDB_EXTRACT data extraction XDS data reduction MOLREP phasing