☰ Navigation Tabs
Crystal structure of HypE-HypF complex
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3VTH 3VTH (chains A and B), 2RB9 (chains C and D) experimental model PDB 2RB9 3VTH (chains A and B), 2RB9 (chains C and D)
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 288 0.1M PIPES, 0.48M KCl, 9% PEG 3350, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 288K
Crystal Properties Matthews coefficient Solvent content 2.56 51.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 118.739 α = 90 b = 119.101 β = 90 c = 174.631 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD RAYONIX MX225HE 2011-12-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL44XU 0.9000 SPring-8 BL44XU
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 2.56 20 100 0.075 12.2 7.1 78733 78733 67
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.6 2.64 100 0.538 4 5.7 3855
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 3VTH (chains A and B), 2RB9 (chains C and D) 2.56 20 74335 3909 97.99 0.20866 0.20643 0.215 0.25064 0.2605 RANDOM 58.492
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] -1.74 3.49 -1.75
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.083 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 15.661 r_dihedral_angle_1_deg 5.3 r_scangle_it 1.768 r_angle_refined_deg 1.077 r_scbond_it 1.017 r_mcangle_it 0.745 r_mcbond_it 0.392 r_chiral_restr 0.074
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.083 r_dihedral_angle_4_deg 17.901 r_dihedral_angle_3_deg 15.661 r_dihedral_angle_1_deg 5.3 r_scangle_it 1.768 r_angle_refined_deg 1.077 r_scbond_it 1.017 r_mcangle_it 0.745 r_mcbond_it 0.392 r_chiral_restr 0.074 r_bond_refined_d 0.008 r_gen_planes_refined 0.004 r_bond_other_d r_angle_other_deg r_gen_planes_other 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_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16538 Nucleic Acid Atoms Solvent Atoms 393 Heterogen Atoms 8
Software Software Software Name Purpose BSS data collection MOLREP phasing REFMAC refinement DENZO data reduction SCALEPACK data scaling