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Crystal structure of the N-terminal signalling domain of human Dhh with calcium
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2WFQ PDB ENTRY 2WFQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 0.1 M TRIS-HCL, PH 8.5 0.2 M LITHIUM SULFATE 0.2 M SODIUM THIOCYANATE 30% (W/V) PEG4000
Crystal Properties Matthews coefficient Solvent content 1.75 34.14
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 40.13 α = 90 b = 41.88 β = 90 c = 83.78 γ = 90
Symmetry Space Group P 21 21 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 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 1.95 40 93.6 0.12 10.5 6.8 10765
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 1.95 2.05 91.8 0.74 2.6 6.5
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 ENTRY 2WFQ 1.95 41.88 10143 491 98.3 0.18196 0.17977 0.1985 0.22487 0.2409 RANDOM 14.375
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] -0.86 1.92 -1.06
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.964 r_dihedral_angle_4_deg 14.624 r_dihedral_angle_3_deg 13.442 r_dihedral_angle_1_deg 5.927 r_scangle_it 3.364 r_scbond_it 2.152 r_angle_refined_deg 1.455 r_mcangle_it 1.295 r_angle_other_deg 0.899 r_mcbond_it 0.752
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.964 r_dihedral_angle_4_deg 14.624 r_dihedral_angle_3_deg 13.442 r_dihedral_angle_1_deg 5.927 r_scangle_it 3.364 r_scbond_it 2.152 r_angle_refined_deg 1.455 r_mcangle_it 1.295 r_angle_other_deg 0.899 r_mcbond_it 0.752 r_mcbond_other 0.202 r_chiral_restr 0.089 r_bond_refined_d 0.014 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001 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_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 1325 Nucleic Acid Atoms Solvent Atoms 96 Heterogen Atoms 13
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction SCALEPACK data scaling PHASER phasing