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Crystal structure of human molybdopterin synthase complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2Q5W 2Q5W:D, 4AP8:A experimental model PDB 4AP8 2Q5W:D, 4AP8:A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 283 12% PEG3350 -- 0.1M potassium nitrate -- 0.05M potassium thiocyanate
Crystal Properties Matthews coefficient Solvent content 3.61 64.21
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 123.72 α = 90 b = 123.72 β = 90 c = 82.49 γ = 120
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 2015-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.97626 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) 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 2.43 61.86 99.9 0.062 0.028 15.8 6.8 27171
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 2.43 2.49 100 0.955 0.472 0.635 1.6 6.1
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 2Q5W:D, 4AP8:A 2.43 61.86 25929 1217 99.91 0.20718 0.20487 0.2137 0.2586 0.2601 RANDOM 59.537
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] -1.51 -0.76 -1.51 4.91
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.772 r_dihedral_angle_4_deg 19.978 r_dihedral_angle_3_deg 15.439 r_long_range_B_refined 9.699 r_long_range_B_other 9.697 r_scangle_other 7.923 r_dihedral_angle_1_deg 7.139 r_mcangle_it 6.931 r_mcangle_other 6.929 r_scbond_it 5.634
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.772 r_dihedral_angle_4_deg 19.978 r_dihedral_angle_3_deg 15.439 r_long_range_B_refined 9.699 r_long_range_B_other 9.697 r_scangle_other 7.923 r_dihedral_angle_1_deg 7.139 r_mcangle_it 6.931 r_mcangle_other 6.929 r_scbond_it 5.634 r_scbond_other 5.632 r_mcbond_other 5.109 r_mcbond_it 5.108 r_angle_refined_deg 1.765 r_angle_other_deg 1.002 r_chiral_restr 0.099 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.002 r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3217 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing