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Human paraplegin, AAA domain in complex with ADP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2CE7 PDB entry 2CE7
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 293 25% PEG 3350, 100mM Bis-Tris pH 6.5, 200mM Ammonium acetate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.22 44.68
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 57.2 α = 90 b = 57.2 β = 90 c = 155.22 γ = 90
Symmetry Space Group P 43 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 4 Toroidal mirror 2007-04-25 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 0.93300 ESRF ID14-2
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 2.2 40 95.1 0.069 0.041 23.7 10.6 13190 13190
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 2.2 2.3 62.7 0.203 0.191 7.2 4.7 1049
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-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 2CE7 2.22 39.13 12529 660 100 0.21153 0.20874 0.2094 0.26171 0.2695 RANDOM 44.905
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.176 r_dihedral_angle_3_deg 17.172 r_dihedral_angle_4_deg 10.286 r_dihedral_angle_1_deg 6.934 r_scangle_it 5.627 r_scbond_it 4.104 r_mcangle_it 2.827 r_mcbond_it 2.015 r_angle_refined_deg 1.603 r_angle_other_deg 0.896
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.176 r_dihedral_angle_3_deg 17.172 r_dihedral_angle_4_deg 10.286 r_dihedral_angle_1_deg 6.934 r_scangle_it 5.627 r_scbond_it 4.104 r_mcangle_it 2.827 r_mcbond_it 2.015 r_angle_refined_deg 1.603 r_angle_other_deg 0.896 r_mcbond_other 0.521 r_symmetry_vdw_other 0.375 r_nbd_refined 0.232 r_nbd_other 0.223 r_xyhbond_nbd_refined 0.208 r_symmetry_hbond_refined 0.195 r_nbtor_refined 0.183 r_nbtor_other 0.093 r_chiral_restr 0.085 r_symmetry_vdw_refined 0.034 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.001 r_gen_planes_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1680 Nucleic Acid Atoms Solvent Atoms 55 Heterogen Atoms 27
Software Software Software Name Purpose REFMAC refinement DNA data collection XDS data reduction XSCALE data scaling MOLREP phasing