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HcgC from Methanococcus maripaludis cocrystallized with SAM and pyridinol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5D4V
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 281 5 mg/ml of pure HcgC containing 2 mM SAM and 2 mM pyridinol was used and mixed at a ratio of 1 ul with 1 ul of precipitant composed of 50% v/v PEG 400, 100 mM NaAcetate pH 4.5 and 200 mM LiSO4
Crystal Properties Matthews coefficient Solvent content 2.17 43.4
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 73.168 α = 90 b = 77.736 β = 110.87 c = 100.991 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 PIXEL DECTRIS PILATUS 6M-F 2016-09-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.99999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 1.75 47.85 99.7 0.082 0.041 0.997 9.7 4.8 106203 29.2
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.75 1.84 100 0.646 0.331 0.421 2.2 4.7
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 5D4V 1.75 47.85 106177 5307 99.6 0.1688 0.1675 0.1801 0.1933 0.2028 RANDOM 37.97
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] -3.4782 0.8315 0.5191 2.9591
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.75 t_omega_torsion 1.47 t_angle_deg 1.21 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 13.75 t_omega_torsion 1.47 t_angle_deg 1.21 t_bond_d 0.01 t_dihedral_angle_d t_incorr_chiral_ct t_pseud_angle t_trig_c_planes t_gen_planes t_it t_nbd t_improper_torsion 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 16869 Nucleic Acid Atoms Solvent Atoms 699 Heterogen Atoms 200
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling MOLREP phasing