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Superoxide dismutase protein from plasmodium berghei
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ISC pdb entry 1ISC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4 277 0.4 ul protein 20 mg/ml, 0.4 ul crystallization buffer, 100mM Zn acetate, 14% PEG 8000, 80mM Na citrate, pH 4.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 3.51 64.94
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 105.111 α = 90 b = 105.111 β = 90 c = 207.935 γ = 120
Symmetry Space Group P 65 2 2
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 2005-03-09 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.2 0.9537 ALS 8.2.2
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 2.33 50 98.7 0.084 25.704 12.9 29521
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 2.33 2.41 86.8 0.465 2.952
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-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 1ISC 2.33 20 29383 1493 98.963 0.1707 0.1794 0.2017 0.2099 random 28.207
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] 1.332 0.666 1.332 -1.997
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.826 r_dihedral_angle_3_deg 12.662 r_dihedral_angle_4_deg 6.173 r_dihedral_angle_1_deg 5.484 r_scangle_it 2.641 r_scbond_it 1.888 r_mcangle_it 1.175 r_scangle_other 1.091 r_angle_refined_deg 1.087 r_mcbond_it 0.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.826 r_dihedral_angle_3_deg 12.662 r_dihedral_angle_4_deg 6.173 r_dihedral_angle_1_deg 5.484 r_scangle_it 2.641 r_scbond_it 1.888 r_mcangle_it 1.175 r_scangle_other 1.091 r_angle_refined_deg 1.087 r_mcbond_it 0.896 r_angle_other_deg 0.707 r_scbond_other 0.57 r_mcangle_other 0.513 r_symmetry_hbond_refined 0.308 r_symmetry_vdw_other 0.223 r_nbd_refined 0.208 r_nbtor_refined 0.19 r_xyhbond_nbd_refined 0.188 r_nbd_other 0.18 r_symmetry_vdw_refined 0.17 r_mcbond_other 0.167 r_nbtor_other 0.089 r_chiral_restr 0.068 r_bond_refined_d 0.01 r_gen_planes_refined 0.004 r_bond_other_d 0.001 r_gen_planes_other
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3133 Nucleic Acid Atoms Solvent Atoms 256 Heterogen Atoms 3
Software Software Software Name Purpose EPMR phasing PDB_EXTRACT data extraction DENZO data reduction SCALEPACK data scaling REFMAC refinement