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Crystal structure of the C-terminal calponin homology domain of alpha parvin
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1WKU PDB ENTRIES 1WKU, 1TJT, 2EYI, 1MB8 experimental model PDB 1TJT PDB ENTRIES 1WKU, 1TJT, 2EYI, 1MB8 experimental model PDB 2EYI PDB ENTRIES 1WKU, 1TJT, 2EYI, 1MB8 experimental model PDB 1MB8 PDB ENTRIES 1WKU, 1TJT, 2EYI, 1MB8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 7.5 12% (W/V) PEG 8000, 35% (V/V) MPD, 0.1M HEPES PH 7.5
Crystal Properties Matthews coefficient Solvent content 2.5 50.36
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.144 α = 90 b = 71.197 β = 99.88 c = 47.146 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 ADSC CCD MIRRORS 2006-11-16 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
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 1.05 23.74 93.7 0.04 16.5 4.2 124910 2
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 1.05 1.11 77.7 0.46 2.4 3.5
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 ENTRIES 1WKU, 1TJT, 2EYI, 1MB8 1.05 46.42 118544 6274 93.5 0.144 0.143 0.1479 0.159 0.1648 RANDOM 9.28
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] 1.09 0.43 -0.87 -0.07
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.608 r_dihedral_angle_4_deg 15.908 r_dihedral_angle_3_deg 12.363 r_dihedral_angle_1_deg 5.319 r_scangle_it 3.605 r_scbond_it 2.946 r_mcangle_it 2.058 r_angle_refined_deg 1.69 r_mcbond_it 1.655 r_angle_other_deg 1.041
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.608 r_dihedral_angle_4_deg 15.908 r_dihedral_angle_3_deg 12.363 r_dihedral_angle_1_deg 5.319 r_scangle_it 3.605 r_scbond_it 2.946 r_mcangle_it 2.058 r_angle_refined_deg 1.69 r_mcbond_it 1.655 r_angle_other_deg 1.041 r_nbd_refined 0.261 r_symmetry_vdw_other 0.244 r_symmetry_vdw_refined 0.241 r_nbd_other 0.195 r_xyhbond_nbd_refined 0.192 r_symmetry_hbond_refined 0.192 r_nbtor_refined 0.19 r_chiral_restr 0.095 r_nbtor_other 0.09 r_bond_refined_d 0.014 r_gen_planes_refined 0.009 r_gen_planes_other 0.004 r_bond_other_d 0.003 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_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 2069 Nucleic Acid Atoms Solvent Atoms 279 Heterogen Atoms 30
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing