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Crystal structure of the human small GTPase GEM
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2RAP 2RAP, 1KAO experimental model PDB 1KAO 2RAP, 1KAO
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 293 PEG3350, Ammonium citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.39 48.58
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 51.242 α = 90 b = 51.242 β = 90 c = 173.873 γ = 90
Symmetry Space Group P 43 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 210 2006-01-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ALS BEAMLINE 8.2.1 1.0 ALS 8.2.1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 50 100 11803
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.25 2.37 100
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) 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 2RAP, 1KAO 2.4 50 9339 9339 463 99.96 0.22039 0.22039 0.21803 0.2126 0.26925 0.2562 RANDOM 42.89
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] 0.9 0.9 -1.8
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.43 r_dihedral_angle_4_deg 19.152 r_dihedral_angle_3_deg 15.415 r_dihedral_angle_1_deg 6.365 r_scangle_it 2.109 r_scbond_it 1.373 r_angle_refined_deg 1.318 r_mcangle_it 0.938 r_angle_other_deg 0.897 r_mcbond_it 0.53
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.43 r_dihedral_angle_4_deg 19.152 r_dihedral_angle_3_deg 15.415 r_dihedral_angle_1_deg 6.365 r_scangle_it 2.109 r_scbond_it 1.373 r_angle_refined_deg 1.318 r_mcangle_it 0.938 r_angle_other_deg 0.897 r_mcbond_it 0.53 r_symmetry_vdw_other 0.197 r_nbd_other 0.192 r_nbd_refined 0.186 r_nbtor_refined 0.169 r_xyhbond_nbd_refined 0.168 r_symmetry_vdw_refined 0.161 r_mcbond_other 0.09 r_nbtor_other 0.085 r_chiral_restr 0.07 r_symmetry_hbond_refined 0.07 r_bond_refined_d 0.011 r_gen_planes_refined 0.004 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1306 Nucleic Acid Atoms Solvent Atoms 35 Heterogen Atoms 28
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction CCP4 data scaling PHASER phasing