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Fasciola hepatica calcium binding protein FhCaBP2: Structure of the dynein light chain-like domain. P6422 native.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 5FWZ PDB ENTRY 5FWZ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 8.5 10 ML OF 10 MM TRIS-HCL PH 8.5, 50 MM SODIUM CHLORIDE, 20 % (W/V) PEG 3350, 0.2 M SODIUM TARTRATE
Crystal Properties Matthews coefficient Solvent content 1.85 33.5
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.63 α = 90 b = 59.63 β = 90 c = 90.062 γ = 120
Symmetry Space Group P 64 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 PIXEL DECTRIS PILATUS 6M SI(111) CHANNEL-CUT, CRYOCOOLEDELLIPTICALLY BENT VERTICAL AND HORIZONTAL FOCUSSING MIRRORS 2015-10-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALBA BEAMLINE XALOC ALBA XALOC
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 2.2 50 100 0.06 22.7 11 5253 41.2
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 2.2 2.32 100 0.49 5 11.7
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 5FWZ 2.3 51.64 4093 484 99.74 0.20938 0.20211 0.2097 0.27491 0.2658 RANDOM 62.215
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] 1.8 0.9 1.8 -5.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.749 r_dihedral_angle_4_deg 22.346 r_dihedral_angle_3_deg 17.22 r_scangle_it 7.95 r_dihedral_angle_1_deg 6.557 r_mcangle_it 6.125 r_scbond_it 5.034 r_mcbond_it 3.856 r_mcbond_other 3.842 r_angle_refined_deg 1.452
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 29.749 r_dihedral_angle_4_deg 22.346 r_dihedral_angle_3_deg 17.22 r_scangle_it 7.95 r_dihedral_angle_1_deg 6.557 r_mcangle_it 6.125 r_scbond_it 5.034 r_mcbond_it 3.856 r_mcbond_other 3.842 r_angle_refined_deg 1.452 r_angle_other_deg 0.944 r_xyhbond_nbd_refined 0.219 r_symmetry_vdw_refined 0.206 r_nbd_refined 0.18 r_nbtor_refined 0.177 r_symmetry_vdw_other 0.164 r_nbd_other 0.163 r_chiral_restr 0.092 r_symmetry_hbond_refined 0.084 r_nbtor_other 0.076 r_xyhbond_nbd_other 0.029 r_bond_refined_d 0.011 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001 r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_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 816 Nucleic Acid Atoms Solvent Atoms 7 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing