☰ Navigation Tabs
H. halophila dodecin in complex with riboflavin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CCB PDB ENTRY 2CCB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 100MM NACL, 100MM KCL, 0.1M ECTOINE, 1MM MGCL2, 20MM HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.43 49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 85.76 α = 90 b = 100.51 β = 90 c = 100.47 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 ADSC CCD MIRRORS 2005-10-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 2.6 20 98.6 0.09 16.9 6.3 26701 3.5
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 2.65 95.7 0.51 3.76 6.5
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 PDB ENTRY 2CCB 2.6 19.96 25902 1370 99.9 0.253 0.251 0.2496 0.288 0.2867 RANDOM 39.47
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] 0.2 -0.2
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.24 r_dihedral_angle_3_deg 22.164 r_dihedral_angle_1_deg 7.155 r_dihedral_angle_4_deg 4.479 r_scangle_it 3.176 r_scbond_it 1.861 r_mcangle_it 1.717 r_angle_refined_deg 1.696 r_mcbond_it 1.01 r_symmetry_vdw_refined 0.541
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.24 r_dihedral_angle_3_deg 22.164 r_dihedral_angle_1_deg 7.155 r_dihedral_angle_4_deg 4.479 r_scangle_it 3.176 r_scbond_it 1.861 r_mcangle_it 1.717 r_angle_refined_deg 1.696 r_mcbond_it 1.01 r_symmetry_vdw_refined 0.541 r_symmetry_hbond_refined 0.412 r_nbtor_refined 0.315 r_nbd_refined 0.208 r_chiral_restr 0.137 r_xyhbond_nbd_refined 0.116 r_bond_refined_d 0.015 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 6267 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms 348
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing