☰ Navigation Tabs
Crystal structure of LumP complexed with flavin mononucleotide
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DDY PDB ENTRY 3DDY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.5 293 20% (w/v) PEG 4000, 0.2M MgCl2, 100mM Tris-HCl pH8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.12 42.05
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.858 α = 90 b = 47.087 β = 90 c = 160.923 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 95 CCD ADSC QUANTUM 210 2008-12-05 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PHOTON FACTORY BEAMLINE AR-NW12A 1.00 Photon Factory AR-NW12A
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 33.22 99.0687 22183
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 3DDY 2 33.22 22183 2496 99.07 0.20226 0.19613 0.1969 0.25523 0.2571 RANDOM 25.7
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.86 r_dihedral_angle_3_deg 17.855 r_dihedral_angle_4_deg 17.674 r_dihedral_angle_1_deg 10.693 r_scangle_it 4.553 r_scbond_it 2.821 r_mcangle_it 2.168 r_angle_refined_deg 1.904 r_mcbond_it 1.319 r_nbtor_refined 0.317
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.86 r_dihedral_angle_3_deg 17.855 r_dihedral_angle_4_deg 17.674 r_dihedral_angle_1_deg 10.693 r_scangle_it 4.553 r_scbond_it 2.821 r_mcangle_it 2.168 r_angle_refined_deg 1.904 r_mcbond_it 1.319 r_nbtor_refined 0.317 r_symmetry_vdw_refined 0.241 r_nbd_refined 0.213 r_symmetry_hbond_refined 0.188 r_xyhbond_nbd_refined 0.165 r_chiral_restr 0.158 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2711 Nucleic Acid Atoms Solvent Atoms 168 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement