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Crystal structure of human unphosphorylated p38gamma
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1CM8
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8 291 1.9 M Sodium Malonate
Crystal Properties Matthews coefficient Solvent content 4.49 72.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 183.631 α = 90 b = 183.631 β = 90 c = 294.242 γ = 120
Symmetry Space Group P 63 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 CCD RAYONIX MX300HE 2016-03-28 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON NSRRC BEAMLINE BL15A1 1.00 NSRRC BL15A1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) CC (Half) 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 3.15 20 100 0.905 21.9 10.9 51419
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Rpim I (All) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 3.15 3.26 100 0.86 11
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 (All) 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 1cm8 3.15 19.944 50783 2558 98.963 0.163 0.1603 0.1655 0.2178 0.2217 Random 65.137
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] -0.069 -0.034 -0.069 0.224
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.315 r_dihedral_angle_3_deg 23.362 r_dihedral_angle_4_deg 22.225 r_lrange_it 13.935 r_lrange_other 13.931 r_scangle_it 9.84 r_scangle_other 9.84 r_mcangle_it 9.411 r_mcangle_other 9.41 r_dihedral_angle_1_deg 8.84
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.315 r_dihedral_angle_3_deg 23.362 r_dihedral_angle_4_deg 22.225 r_lrange_it 13.935 r_lrange_other 13.931 r_scangle_it 9.84 r_scangle_other 9.84 r_mcangle_it 9.411 r_mcangle_other 9.41 r_dihedral_angle_1_deg 8.84 r_scbond_it 6.264 r_scbond_other 6.263 r_mcbond_it 6.054 r_mcbond_other 6.053 r_angle_refined_deg 1.739 r_angle_other_deg 1.278 r_nbd_other 0.225 r_nbd_refined 0.22 r_symmetry_nbd_other 0.199 r_symmetry_nbd_refined 0.183 r_nbtor_refined 0.174 r_xyhbond_nbd_refined 0.172 r_symmetry_xyhbond_nbd_refined 0.162 r_symmetry_nbtor_other 0.087 r_chiral_restr 0.079 r_symmetry_xyhbond_nbd_other 0.016 r_bond_refined_d 0.008 r_gen_planes_refined 0.007 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11192 Nucleic Acid Atoms Solvent Atoms 230 Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement HKL-2000 data reduction HKL-2000 data scaling MOLREP phasing