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Crystal structure of LumP complexed with riboflavin
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 6.8 293 20% (w/v) PEG 4000, 0.2M MgCl2, 100mM HEPES pH6.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.08 40.74
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 46.288 α = 90 b = 46.582 β = 90 c = 161.053 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 RIGAKU JUPITER 210 monochromator 2008-08-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SPRING-8 BEAMLINE BL26B1 1.00 SPring-8 BL26B1
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 1.421 25.559 58164
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 1.421 20.15 58164 6533 97.12 0.19632 0.19206 0.19 0.23443 0.2331 RANDOM 23.28
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] -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.332 r_dihedral_angle_4_deg 21.234 r_dihedral_angle_3_deg 16.539 r_dihedral_angle_1_deg 9.927 r_scangle_it 5.998 r_scbond_it 4.015 r_mcangle_it 2.967 r_angle_refined_deg 2.896 r_mcbond_it 1.991 r_chiral_restr 0.353
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.332 r_dihedral_angle_4_deg 21.234 r_dihedral_angle_3_deg 16.539 r_dihedral_angle_1_deg 9.927 r_scangle_it 5.998 r_scbond_it 4.015 r_mcangle_it 2.967 r_angle_refined_deg 2.896 r_mcbond_it 1.991 r_chiral_restr 0.353 r_nbtor_refined 0.327 r_symmetry_vdw_refined 0.308 r_nbd_refined 0.242 r_symmetry_hbond_refined 0.204 r_xyhbond_nbd_refined 0.16 r_bond_refined_d 0.033 r_gen_planes_refined 0.015 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 2832 Nucleic Acid Atoms Solvent Atoms 405 Heterogen Atoms 54
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing