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Crystal structure of human Mps1 catalytic domain in complex with ATP
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 2.64 53.49
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 70.98 α = 90 b = 104.95 β = 90 c = 111.02 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 94 IMAGE PLATE RIGAKU RAXIS IV++ 2008-10-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 1.5418
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 2.7 40.36 97.8 0.072 0.079 21.2 5.7 11436 1 75.912
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 2.7 2.85 97 0.519 0.232 3 5.8 9374
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 2.7 40.36 10890 545 97.44 0.22288 0.22072 0.2228 0.26457 0.2697 RANDOM 45.162
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] -2.75 -0.54 3.29
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.066 r_dihedral_angle_4_deg 24.509 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_1_deg 5.335 r_angle_refined_deg 0.973 r_scangle_it 0.858 r_angle_other_deg 0.773 r_scbond_it 0.557 r_mcangle_it 0.53 r_mcbond_it 0.484
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.066 r_dihedral_angle_4_deg 24.509 r_dihedral_angle_3_deg 13.562 r_dihedral_angle_1_deg 5.335 r_angle_refined_deg 0.973 r_scangle_it 0.858 r_angle_other_deg 0.773 r_scbond_it 0.557 r_mcangle_it 0.53 r_mcbond_it 0.484 r_nbd_refined 0.198 r_symmetry_vdw_other 0.193 r_symmetry_vdw_refined 0.182 r_symmetry_hbond_refined 0.18 r_nbtor_refined 0.17 r_nbd_other 0.164 r_xyhbond_nbd_refined 0.118 r_nbtor_other 0.081 r_chiral_restr 0.057 r_mcbond_other 0.042 r_bond_refined_d 0.007 r_gen_planes_refined 0.002 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2083 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 47
Software Software Software Name Purpose CrystalClear data collection MOLREP phasing REFMAC refinement MOSFLM data reduction SCALA data scaling