☰ Navigation Tabs
Human mesencephalic astrocyte-derived neurotrophic factor (MANF)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details other CDNF N-TERMINAL DOMAIN
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 277 NEEDLE CRYSTALS OF MANF WERE TYPICALLY OBTAINED WITHIN 1 TO 2 WEEKS AT 4 C OVER A RESERVOIR SOLUTION OF 100 MM SODIUM CACODYLATE BUFFER, PH 6.5, 0.2 M MGAC2 AND 12-18 % PEG 8000.
Crystal Properties Matthews coefficient Solvent content 3 53
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 96.5 α = 90 b = 96.5 β = 90 c = 35.05 γ = 120
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 93 CCD ADSC CCD M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-1 ESRF ID23-1
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 2.8 20 97 0.04 20.1 7 32978 -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 2.8 2.9 94 0.54 2.6
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 CDNF N-TERMINAL DOMAIN 2.8 19.87 4457 216 98.4 0.281 0.28 0.277 0.305 0.294 RANDOM 83.85
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] -0.05 -0.03 -0.05 0.08
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.001 r_dihedral_angle_3_deg 17.619 r_dihedral_angle_4_deg 16.708 r_dihedral_angle_1_deg 5.121 r_scangle_it 1.164 r_angle_refined_deg 0.978 r_mcangle_it 0.761 r_scbond_it 0.655 r_mcbond_it 0.408 r_nbtor_refined 0.298
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.001 r_dihedral_angle_3_deg 17.619 r_dihedral_angle_4_deg 16.708 r_dihedral_angle_1_deg 5.121 r_scangle_it 1.164 r_angle_refined_deg 0.978 r_mcangle_it 0.761 r_scbond_it 0.655 r_mcbond_it 0.408 r_nbtor_refined 0.298 r_nbd_refined 0.211 r_symmetry_vdw_refined 0.197 r_xyhbond_nbd_refined 0.106 r_chiral_restr 0.068 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 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_refined 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 975 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XDS data scaling MOLREP phasing