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Fresh crystals of HcgC from Methanococcus maripaludis cocrystallized with SAH and pyridinol
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5O4H
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7.5 281 The drop consists of 1 ul of enzyme solution containing ~5 mg/ml HcgC, 2 mM pyridinol (dissolved in 100% DMSO) and 2 mM SAH mixed with 1 ul of the reservoir solution : 100 mM HEPES/NaOH pH 7.5, 0.1 M NaCl, and 30% 2-Methyl-2,4-pentanediol. After only 4 days the crystals were immediately fished and frozen in liquid nitrogen for synchrotron radiation.
Crystal Properties Matthews coefficient Solvent content 2.29 46.3
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.875 α = 90 b = 83.536 β = 109.54 c = 99.987 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 2017-02-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.00001 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 2.1 47.11 97.9 0.054 0.039 0.998 11.5 2.6 63739 40.63
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 2.1 2.21 98.8 0.544 0.412 0.804 1.7 2.5
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 5O4H 2.1 46.68 63705 3141 97.75 0.2037 0.2022 0.2095 0.2335 0.2327 RANDOM 56.2
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] 1.3751 0.8339 -1.1305 -0.2446
RMS Deviations Key Refinement Restraint Deviation t_other_torsion 14.19 t_omega_torsion 1.32 t_angle_deg 1.19 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 14.19 t_omega_torsion 1.32 t_angle_deg 1.19 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 16861 Nucleic Acid Atoms Solvent Atoms 522 Heterogen Atoms 208
Software Software Software Name Purpose BUSTER refinement XDS data reduction SCALA data scaling MOLREP phasing