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Crystal structure of Human Senescence Marker Protein-30 (Zinc Bound)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3G4E PDB ENTRY 3G4E
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.8 298 38% PEG 6000, 0.1M Tris-Hcl, 5mM DTT, 5mM CaCl2, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.12 42.11
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 64.365 α = 90 b = 52.019 β = 100.11 c = 85.832 γ = 90
Symmetry Space Group P 1 21 1
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 MAR CCD 165 mm 2007-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 31-ID APS 31-ID
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.92 84.52 99 0.086 0.086 5.251 7 42805
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.92 2.02 94 0.013 0.01286 0.5 6.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) 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 3G4E 1.92 84.52 42738 40630 2108 99.23 0.22519 0.22372 0.2394 0.25336 0.3077 RANDOM 43.462
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] 1.9 1.66 1.08 -2.4
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.287 r_sphericity_free 26.875 r_sphericity_bonded 24.469 r_dihedral_angle_4_deg 21.239 r_dihedral_angle_3_deg 18.166 r_dihedral_angle_1_deg 11.38 r_scangle_it 7.244 r_scbond_it 5.525 r_rigid_bond_restr 4.497 r_mcangle_it 4.362
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.287 r_sphericity_free 26.875 r_sphericity_bonded 24.469 r_dihedral_angle_4_deg 21.239 r_dihedral_angle_3_deg 18.166 r_dihedral_angle_1_deg 11.38 r_scangle_it 7.244 r_scbond_it 5.525 r_rigid_bond_restr 4.497 r_mcangle_it 4.362 r_mcbond_it 3.287 r_angle_refined_deg 2.582 r_nbtor_refined 0.314 r_symmetry_vdw_refined 0.291 r_nbd_refined 0.261 r_symmetry_hbond_refined 0.196 r_chiral_restr 0.184 r_xyhbond_nbd_refined 0.176 r_bond_refined_d 0.035 r_gen_planes_refined 0.013 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
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 4606 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 2
Software Software Software Name Purpose MOSFLM data reduction SCALA data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction