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HcgB from Methanocaldococcus jannaschii in complex with the guanylyl-pyridinol product in a model reaction of [Fe]-hydrogenase cofactor biosynthesis
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3WB1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 20%(w/v) PEG 8000, 0.1M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.36 47.81
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 115.01 α = 90 b = 97.37 β = 90 c = 63.54 γ = 90
Symmetry Space Group P 21 21 2
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 2012-02-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.9999 SLS X10SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) 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 2.4 50 99.3 0.09 14.53 27204 -3 47.414
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.4 2.5 95.7 0.779 0.865 2.39
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 3WB1 2.44 49.51 27164 1362 99.31 0.1745 0.1717 0.1718 0.2263 0.2255 RANDOM 43.5211
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] -0.04 0.05 -0.02
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.094 r_dihedral_angle_3_deg 21.039 r_dihedral_angle_4_deg 18.138 r_dihedral_angle_1_deg 6.251 r_scbond_it 4.329 r_mcangle_it 3.756 r_mcbond_it 2.516 r_angle_refined_deg 1.968 r_chiral_restr 0.125 r_bond_refined_d 0.016
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.094 r_dihedral_angle_3_deg 21.039 r_dihedral_angle_4_deg 18.138 r_dihedral_angle_1_deg 6.251 r_scbond_it 4.329 r_mcangle_it 3.756 r_mcbond_it 2.516 r_angle_refined_deg 1.968 r_chiral_restr 0.125 r_bond_refined_d 0.016 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4986 Nucleic Acid Atoms Solvent Atoms 136 Heterogen Atoms 162
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling