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Crystal structure of mouse Ces2c
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1MX9
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 293.15 Crystallisation condition 0.5 ul with PEG 8000, 0.2 M Ammonium sulfate 0.1 M Sodium cacodylate, pH-6.5, 30 % w/v and 0.5 ul 10mg/ml Protein in 150mM NaCl, 20mM Tris HCl
Crystal Properties Matthews coefficient Solvent content 2.5 50.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 98.052 α = 90 b = 143.595 β = 90 c = 183.756 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 PIXEL DECTRIS EIGER2 X 16M 2021-05-10 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON PETRA III, DESY BEAMLINE P11 1.012100 PETRA III, DESY P11
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) CC (Half) 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 2.12 49.05 98.99 0.0906 0.998 15.23 6.9 145761
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.12 2.196 97.4 0.5328 0.881 6.3
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 (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1MX9 2.12 49.05 145757 7342 99.004 0.165 0.163 0.163 0.1959 0.1959 33.15
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] 0.009 0.008 -0.017
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.54 r_dihedral_angle_4_deg 18.778 r_dihedral_angle_3_deg 11.596 r_lrange_it 8.16 r_lrange_other 8.093 r_dihedral_angle_1_deg 6.685 r_scangle_it 6.358 r_scangle_other 6.357 r_mcangle_other 4.247 r_mcangle_it 4.246
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 31.54 r_dihedral_angle_4_deg 18.778 r_dihedral_angle_3_deg 11.596 r_lrange_it 8.16 r_lrange_other 8.093 r_dihedral_angle_1_deg 6.685 r_scangle_it 6.358 r_scangle_other 6.357 r_mcangle_other 4.247 r_mcangle_it 4.246 r_scbond_it 4.097 r_scbond_other 4.096 r_mcbond_it 2.951 r_mcbond_other 2.948 r_angle_other_deg 2.303 r_angle_refined_deg 1.534 r_nbd_other 0.265 r_symmetry_nbd_refined 0.256 r_nbd_refined 0.221 r_symmetry_nbd_other 0.207 r_nbtor_refined 0.163 r_xyhbond_nbd_refined 0.161 r_symmetry_xyhbond_nbd_refined 0.132 r_ncsr_local_group_1 0.09 r_chiral_restr 0.083 r_ncsr_local_group_2 0.078 r_ncsr_local_group_3 0.078 r_ncsr_local_group_4 0.078 r_ncsr_local_group_6 0.074 r_ncsr_local_group_5 0.069 r_symmetry_nbtor_other 0.066 r_bond_other_d 0.035 r_gen_planes_other 0.011 r_bond_refined_d 0.01 r_gen_planes_refined 0.008
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 16161 Nucleic Acid Atoms Solvent Atoms 1517 Heterogen Atoms 63
Software Software Software Name Purpose REFMAC refinement XDS data reduction Aimless data scaling PHASER phasing Coot model building