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Crystal structure of the unliganded form of HCN2 CNBD
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1ANF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 34-36% dimethyl PEG 500, 240 mM potassium nitrate, 20 mM magnesium chloride, 100 mM BIS-TRIS, pH 6.0
Crystal Properties Matthews coefficient Solvent content 2.24 44.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 61.517 α = 90 b = 42.01 β = 90.85 c = 198.376 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 MARMOSAIC 300 mm CCD 2015-04-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97933 APS 23-ID-B
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 2.04 25 99.9 0.115 7.6 3.4 62519 -3 31.3
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 2.04 2.11 100 0.667 2.3 3.4
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 1ANF 2.042 24.82 59374 3134 95.68 0.18237 0.18036 0.1865 0.22084 0.2227 RANDOM 28.299
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] -0.76 -0.33 -13.42 14.18
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.019 r_dihedral_angle_4_deg 14.617 r_dihedral_angle_3_deg 14.341 r_dihedral_angle_1_deg 5.835 r_long_range_B_refined 5.693 r_long_range_B_other 5.661 r_scangle_other 3.796 r_mcangle_it 2.573 r_mcangle_other 2.573 r_scbond_it 2.206
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 34.019 r_dihedral_angle_4_deg 14.617 r_dihedral_angle_3_deg 14.341 r_dihedral_angle_1_deg 5.835 r_long_range_B_refined 5.693 r_long_range_B_other 5.661 r_scangle_other 3.796 r_mcangle_it 2.573 r_mcangle_other 2.573 r_scbond_it 2.206 r_scbond_other 2.206 r_mcbond_it 1.517 r_mcbond_other 1.517 r_angle_refined_deg 1.322 r_angle_other_deg 1.005 r_chiral_restr 0.074 r_bond_refined_d 0.009 r_gen_planes_refined 0.005 r_bond_other_d 0.002 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_scangle_it r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7879 Nucleic Acid Atoms Solvent Atoms 369 Heterogen Atoms 58
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling PHASER phasing