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Crystal structure of the FGFR2 D2 domain
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3CAF PDB ENTRY 3CAF
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 293 1.8M ammonium citrate dibasic, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 3.16 61.13
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 106.1 α = 90 b = 42.46 β = 124.99 c = 79.62 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 293 CCD RIGAKU SATURN 944 2006-11-19 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU MICROMAX-007 HF 1.5418
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 2.34 22.18 0.109 4.9 3.1 12416
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) 2.34 2.42 0.425 2.2 3.02 1240
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 3CAF 2.34 22.18 10631 533 89.38 0.1858 0.18368 0.186 0.22772 0.2324 RANDOM 32.801
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]
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.755 r_dihedral_angle_4_deg 13.598 r_dihedral_angle_3_deg 13.022 r_scangle_it 4.8 r_mcangle_it 4.453 r_scbond_it 3.211 r_dihedral_angle_1_deg 2.939 r_mcbond_it 2.893 r_angle_refined_deg 2.275 r_nbtor_refined 0.323
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 27.755 r_dihedral_angle_4_deg 13.598 r_dihedral_angle_3_deg 13.022 r_scangle_it 4.8 r_mcangle_it 4.453 r_scbond_it 3.211 r_dihedral_angle_1_deg 2.939 r_mcbond_it 2.893 r_angle_refined_deg 2.275 r_nbtor_refined 0.323 r_nbd_refined 0.271 r_chiral_restr 0.187 r_xyhbond_nbd_refined 0.186 r_symmetry_vdw_refined 0.183 r_symmetry_hbond_refined 0.09 r_bond_refined_d 0.038 r_gen_planes_refined 0.012 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 1628 Nucleic Acid Atoms Solvent Atoms 101 Heterogen Atoms
Software Software Software Name Purpose CrystalClear data collection PHASES phasing REFMAC refinement CrystalClear data reduction CrystalClear data scaling