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Crystal structure of human Mps1 catalytic domain in complex with a quinazolin ligand Compound 4
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2ZMD PDB ENTRY 2ZMD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 293 20 % PEG 300, 0.1 M HEPES, 2.5 % Isopropanol, 5 % Glycerol, 50 mM Ammonium sulphate, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.65 53.59
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 71.37 α = 90 b = 103.93 β = 90 c = 111.73 γ = 90
Symmetry Space Group I 2 2 2
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 QUANTUM 315 2008-09-14 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON DIAMOND BEAMLINE I03 0.9200 Diamond I03
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym 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 2.3 60.15 98.4 0.073 0.079 17.7 6.3 18501 1 42.213
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.3 2.42 90.3 0.39 0.454 3 3.9 9288
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 2ZMD 2.3 60.15 17558 942 98.14 0.2117 0.20977 0.2075 0.24762 0.2405 RANDOM 30.476
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] -1.32 -0.21 1.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.112 r_dihedral_angle_4_deg 25.236 r_dihedral_angle_3_deg 13.875 r_dihedral_angle_1_deg 5.81 r_scangle_it 1.832 r_scbond_it 1.246 r_angle_refined_deg 1.17 r_mcangle_it 1.018 r_mcbond_it 0.917 r_angle_other_deg 0.853
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 41.112 r_dihedral_angle_4_deg 25.236 r_dihedral_angle_3_deg 13.875 r_dihedral_angle_1_deg 5.81 r_scangle_it 1.832 r_scbond_it 1.246 r_angle_refined_deg 1.17 r_mcangle_it 1.018 r_mcbond_it 0.917 r_angle_other_deg 0.853 r_symmetry_vdw_other 0.213 r_nbd_refined 0.189 r_nbd_other 0.184 r_nbtor_refined 0.172 r_symmetry_hbond_refined 0.164 r_xyhbond_nbd_refined 0.142 r_symmetry_vdw_refined 0.142 r_mcbond_other 0.104 r_nbtor_other 0.086 r_chiral_restr 0.072 r_bond_refined_d 0.009 r_gen_planes_refined 0.003 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2107 Nucleic Acid Atoms Solvent Atoms 85 Heterogen Atoms 69
Software Software Software Name Purpose ADSC data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling