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Crystal structure of the kinase domain of MPP1/p55
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1KGD pdb entry 1KGD
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5.5 291 1.6M ammonium sulfate, 0.01M magnesium chloride, 0.1M sodium cacodylate. The sample solution also contained 0.002M GDP, 0.002M ADP, 0.005M magnesium chloride. Crystal growth was incubated for 5 months., pH 5.5, vapor diffusion, sitting drop, temperature 291K
Crystal Properties Matthews coefficient Solvent content 4.15 73
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 72.088 α = 90 b = 131.562 β = 90 c = 237.19 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 CCD RAYONIX MX-300 2010-05-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CLSI BEAMLINE 08ID-1 0.97949 CLSI 08ID-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 2.25 40 99.9 0.165 6.6 6 106079
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 2.25 2.33 98.7 0.963 4.9 10330
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 1KGD 2.26 30 105554 2121 99.254 0.236 0.235 0.2336 0.271 0.2713 RANDOM 24.726
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] -2.158 0.399 1.759
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.172 r_dihedral_angle_4_deg 19.296 r_dihedral_angle_3_deg 14.167 r_dihedral_angle_1_deg 6.032 r_scangle_it 4.354 r_scbond_it 2.581 r_mcangle_it 1.746 r_angle_refined_deg 1.456 r_mcbond_it 0.894 r_angle_other_deg 0.866
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.172 r_dihedral_angle_4_deg 19.296 r_dihedral_angle_3_deg 14.167 r_dihedral_angle_1_deg 6.032 r_scangle_it 4.354 r_scbond_it 2.581 r_mcangle_it 1.746 r_angle_refined_deg 1.456 r_mcbond_it 0.894 r_angle_other_deg 0.866 r_mcbond_other 0.167 r_chiral_restr 0.084 r_bond_refined_d 0.016 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 8355 Nucleic Acid Atoms Solvent Atoms 201 Heterogen Atoms 91
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling MOLREP phasing REFMAC refinement PDB_EXTRACT data extraction HKL-2000 data reduction HKL-2000 data scaling