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Crystal structure of human SENP1 with the bound cobalt
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2IYC PDB ENTRY 2IYC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 CRYSTALS FORMED FROM 1 TO 1 OF RESERVOIR SOLUTION (1.8 M AMMONIUM SULFATE, 50 MM COCL2 AND 100 MM MES PH 6.5) AND PROTEIN SOLUTION (20 MG/ML IN 20 MM TRIS/HCL (PH 8.0), AND 50 MM NACL).
Crystal Properties Matthews coefficient Solvent content 2.6 52.76
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.172 α = 90 b = 71.172 β = 90 c = 199.988 γ = 120
Symmetry Space Group P 31 2 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 ADSC CCD 2010-02-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID29 ESRF ID29
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 2.4 45 99.8 0.09 8.5 5.1 23808 2 53.9
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 2.4 2.53 100 0.43 2.5 5.2
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 PDB ENTRY 2IYC 2.4 66.66 22537 1217 99.71 0.23137 0.22702 0.31339 0.2513 RANDOM 58.721
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] 1.24 0.62 1.24 -1.87
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.419 r_dihedral_angle_3_deg 19.878 r_dihedral_angle_4_deg 17.659 r_scangle_it 8.495 r_dihedral_angle_1_deg 6.696 r_scbond_it 6.399 r_mcangle_it 4.233 r_mcbond_it 2.421 r_angle_refined_deg 1.639 r_chiral_restr 0.119
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.419 r_dihedral_angle_3_deg 19.878 r_dihedral_angle_4_deg 17.659 r_scangle_it 8.495 r_dihedral_angle_1_deg 6.696 r_scbond_it 6.399 r_mcangle_it 4.233 r_mcbond_it 2.421 r_angle_refined_deg 1.639 r_chiral_restr 0.119 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3790 Nucleic Acid Atoms Solvent Atoms 70 Heterogen Atoms 37
Software Software Software Name Purpose REFMAC refinement iMOSFLM data reduction SCALA data scaling PHASER phasing