☰ Navigation Tabs
HcgB from Methanocaldococcus jannaschii in complex with light-decomposed FeGP cofactor of [Fe]-hydrogenase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3BRC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 298 20 %(w/v) PEG 8000, 0.1 M sodium cacodylate, 0.2M magnesium acetate, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.11 41.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.96 α = 90 b = 119.34 β = 115.14 c = 55.65 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 2012-06-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 1.000 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 1.9 50 94.9 0.085 11.17 46660 -3 30.577
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 1.9 2 87.7 0.323 0.412 2.88
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 3BRC 1.91 47.94 45988 2329 94.26 0.2291 0.2266 0.2251 0.2752 0.273 RANDOM 29.9177
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] -0.08 0.07 0.1 -0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.394 r_dihedral_angle_3_deg 18.138 r_dihedral_angle_4_deg 17.058 r_dihedral_angle_1_deg 6.166 r_scbond_it 3.177 r_mcangle_it 2.652 r_angle_refined_deg 2.031 r_mcbond_it 1.87 r_chiral_restr 0.131 r_bond_refined_d 0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.394 r_dihedral_angle_3_deg 18.138 r_dihedral_angle_4_deg 17.058 r_dihedral_angle_1_deg 6.166 r_scbond_it 3.177 r_mcangle_it 2.652 r_angle_refined_deg 2.031 r_mcbond_it 1.87 r_chiral_restr 0.131 r_bond_refined_d 0.017 r_gen_planes_refined 0.009
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4956 Nucleic Acid Atoms Solvent Atoms 376 Heterogen Atoms 148
Software Software Software Name Purpose XSCALE data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction XDS data scaling