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crystal structure of RluD from E. coli
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 8.6 298 equal parts protein (~3mg/ml) and precipitant 12-18% PEG 4000, 100 mM Tris, pH 8.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.93 57.97
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 67.32 α = 90 b = 75.14 β = 90 c = 85.8 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 103 M MAD 2 1 x-ray 103 M SINGLE WAVELENGTH 1,2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL7-1 SSRL BL7-1 2 SYNCHROTRON SSRL BEAMLINE BL7-1 SSRL BL7-1
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 1.86 53 36440 36440 -3 -3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 MAD combined with MIR THROUGHOUT 1.86 53 36440 36440 3638 97.7 0.204 0.199 0.199 0.1989 0.241 0.2403 RANDOM 31.286
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] -0.18 -0.4 0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.489 r_dihedral_angle_4_deg 18.88 r_dihedral_angle_3_deg 14.856 r_dihedral_angle_1_deg 6.298 r_scangle_it 4.142 r_scbond_it 2.712 r_mcangle_it 1.699 r_angle_refined_deg 1.625 r_mcbond_it 1.108 r_nbtor_refined 0.299
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.489 r_dihedral_angle_4_deg 18.88 r_dihedral_angle_3_deg 14.856 r_dihedral_angle_1_deg 6.298 r_scangle_it 4.142 r_scbond_it 2.712 r_mcangle_it 1.699 r_angle_refined_deg 1.625 r_mcbond_it 1.108 r_nbtor_refined 0.299 r_nbd_refined 0.209 r_symmetry_vdw_refined 0.196 r_xyhbond_nbd_refined 0.182 r_chiral_restr 0.115 r_symmetry_hbond_refined 0.104 r_bond_refined_d 0.017 r_gen_planes_refined 0.007
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2568 Nucleic Acid Atoms Solvent Atoms 251 Heterogen Atoms 9
Software Software Software Name Purpose REFMAC refinement PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling SOLVE phasing