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Crystal Structure of the Autoinhibited Human c-Fms Kinase Domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1RJB PDB entry 1RJB
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.2 293 30% PEG 8000, 0.2M Ammonium sulfate, 0.1M MES pH 6.2, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.37 48.07
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 104.253 α = 90 b = 57.298 β = 90 c = 56.785 γ = 90
Symmetry Space Group P 21 21 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 4 2006-04-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 14-BM-C 0.90000 APS 14-BM-C
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 2.7 50 0.113 22.9 6.58 9841
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.7 2.8 7.8
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 1RJB 2.7 25.44 9333 472 99.65 0.20966 0.20617 0.2109 0.27926 0.2643 RANDOM 31.932
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] -0.08 0.04 0.04
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.397 r_dihedral_angle_3_deg 16.838 r_dihedral_angle_4_deg 16.304 r_dihedral_angle_1_deg 6.565 r_scangle_it 3.471 r_scbond_it 2.238 r_mcangle_it 1.791 r_angle_refined_deg 1.31 r_mcbond_it 0.955 r_nbtor_refined 0.302
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.397 r_dihedral_angle_3_deg 16.838 r_dihedral_angle_4_deg 16.304 r_dihedral_angle_1_deg 6.565 r_scangle_it 3.471 r_scbond_it 2.238 r_mcangle_it 1.791 r_angle_refined_deg 1.31 r_mcbond_it 0.955 r_nbtor_refined 0.302 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.161 r_symmetry_hbond_refined 0.141 r_chiral_restr 0.129 r_xyhbond_nbd_refined 0.105 r_bond_refined_d 0.007 r_gen_planes_refined 0.003 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_other r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2468 Nucleic Acid Atoms Solvent Atoms 91 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data collection HKL-2000 data reduction CCP4 data scaling PHASES phasing