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Methyltransferase domain of human Wolf-Hirschhorn Syndrome Candidate 1-Like protein 1 (WHSC1L1)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3OOI pdb entry 3OOI
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 6.5 293 20% PEG-5000-MME, 0.1 M bis-tris, 0.02 M sarcosine
Crystal Properties Matthews coefficient Solvent content 2.41 48.87
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 44.16 α = 90 b = 62.81 β = 109.78 c = 48.84 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 RAYONIX MX-300 2015-01-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97957 CLSI 08ID-1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) 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 1.8 41.55 98.9 0.105 0.124 0.064 0.995 11.1 3.7 23067
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rrim I (All) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.8 1.85 96.2 0.714 0.859 0.471 0.626 3.2 1678
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-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT pdb entry 3OOI 1.8 41.55 21949 1118 98.79 0.1856 0.1839 0.2182 0.2031 24.398
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] 1.35 0.47 -0.52 -0.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.055 r_dihedral_angle_4_deg 21.717 r_dihedral_angle_3_deg 13.356 r_dihedral_angle_1_deg 6.008 r_mcangle_it 3.416 r_mcbond_it 2.221 r_mcbond_other 2.221 r_angle_refined_deg 1.801 r_angle_other_deg 1.033 r_chiral_restr 0.109
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 30.055 r_dihedral_angle_4_deg 21.717 r_dihedral_angle_3_deg 13.356 r_dihedral_angle_1_deg 6.008 r_mcangle_it 3.416 r_mcbond_it 2.221 r_mcbond_other 2.221 r_angle_refined_deg 1.801 r_angle_other_deg 1.033 r_chiral_restr 0.109 r_bond_refined_d 0.016 r_gen_planes_refined 0.008 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1644 Nucleic Acid Atoms Solvent Atoms 144 Heterogen Atoms 47
Software Software Software Name Purpose REFMAC refinement Aimless data scaling PDB_EXTRACT data extraction xia2 data reduction XDS data reduction PHASER phasing