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Crystal structure of the C-terminal calponin homology domain of alpha- parvin in complex with paxillin LD2 motif
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2VZC PDB ENTRY 2VZC
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 4.5 286 40% (W/V) PEG200, 0.1 M CITRATE PH 4.5
Crystal Properties Matthews coefficient Solvent content 2.2 43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 74.008 α = 90 b = 94.422 β = 90 c = 41.841 γ = 90
Symmetry Space Group C 2 2 21
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 2007-08-02 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I04 Diamond I04
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 1.8 27.71 99.6 0.07 13.2 3.4 13920 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 1.8 1.9 100 0.35 3.2 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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 2VZC 1.8 58.22 13218 690 99.4 0.187 0.186 0.221 0.2376 RANDOM 25.44
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] 1.11 -0.84 -0.28
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.433 r_dihedral_angle_4_deg 24.915 r_dihedral_angle_3_deg 12.536 r_dihedral_angle_1_deg 4.401 r_scangle_it 2.222 r_scbond_it 1.56 r_angle_refined_deg 1.225 r_mcangle_it 0.93 r_mcbond_it 0.557 r_nbtor_refined 0.301
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.433 r_dihedral_angle_4_deg 24.915 r_dihedral_angle_3_deg 12.536 r_dihedral_angle_1_deg 4.401 r_scangle_it 2.222 r_scbond_it 1.56 r_angle_refined_deg 1.225 r_mcangle_it 0.93 r_mcbond_it 0.557 r_nbtor_refined 0.301 r_symmetry_vdw_refined 0.239 r_nbd_refined 0.214 r_xyhbond_nbd_refined 0.181 r_symmetry_hbond_refined 0.142 r_chiral_restr 0.086 r_bond_refined_d 0.01 r_gen_planes_refined 0.005 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 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 1149 Nucleic Acid Atoms Solvent Atoms 65 Heterogen Atoms 43
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing