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Crystal structure of a novel family of manganese-containing cupin (tm1459) from thermotoga maritima at 1.65 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FI2
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION,SITTING DROP,NANODROP 5.2 293 50% (v/v) PEG-200, 0.1M Phosphate-citrate pH 4.2 0.2M NaCl, pH 5.2, VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.71 54.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 52.55 α = 90 b = 52.55 β = 90 c = 96.267 γ = 120
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 QUANTUM 315 flat mirror 2002-01-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRL BEAMLINE BL11-1 SSRL BL11-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 1.65 48.13 97.8 0.057 15.6 3.6 35029 35029 30.49
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.65 1.74 87.6 0.466 1.9 2.7 4592
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 1FI2 1.65 33.07 33262 1729 97.78 0.21015 0.20817 0.24859 0.1986 RANDOM 24.615
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] 0.98 0.49 0.98 -1.47
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.829 r_dihedral_angle_4_deg 23.596 r_dihedral_angle_3_deg 18.157 r_dihedral_angle_1_deg 6.971 r_scangle_it 3.338 r_scbond_it 2.509 r_angle_refined_deg 1.652 r_mcangle_it 1.351 r_mcbond_it 1.179 r_angle_other_deg 0.854
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.829 r_dihedral_angle_4_deg 23.596 r_dihedral_angle_3_deg 18.157 r_dihedral_angle_1_deg 6.971 r_scangle_it 3.338 r_scbond_it 2.509 r_angle_refined_deg 1.652 r_mcangle_it 1.351 r_mcbond_it 1.179 r_angle_other_deg 0.854 r_symmetry_vdw_other 0.272 r_nbd_other 0.193 r_nbd_refined 0.186 r_symmetry_hbond_refined 0.151 r_symmetry_vdw_refined 0.137 r_chiral_restr 0.103 r_nbtor_other 0.091 r_xyhbond_nbd_refined 0.054 r_bond_refined_d 0.018 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1850 Nucleic Acid Atoms Solvent Atoms 169 Heterogen Atoms 6
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling MOLREP phasing REFMAC refinement CCP4 data scaling