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Crystal Structure of Human GTPase IMAP family member 1
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3LXX unpublished model of GIMAP4. Related to PDB entry 3LXX.
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION 7.5 293 25% w/v PEG3350, 0.2M sodium chloride, 0.1M HEPES. GDP and 1:100 dispase were also added., pH 7.5, vapor diffusion, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.06 47.9
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 81.348 α = 90 b = 81.348 β = 90 c = 178.934 γ = 120
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 MARMOSAIC 300 mm CCD 2009-11-20 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 23-ID-B 0.97948 APS 23-ID-B
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 2.2 50 97.1 0.098 9 4.1 21552
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 2.2 2.24 75.6 0.422 1.9 851
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(Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT unpublished model of GIMAP4. Related to PDB entry 3LXX. 2.206 29.822 21544 1045 96.818 0.214 0.2125 0.2112 0.246 0.2439 THIN SHELLS (SFTOOLS) 32.343
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] -0.02 -0.01 -0.02 0.03
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.87 r_dihedral_angle_4_deg 20.165 r_dihedral_angle_3_deg 14.129 r_dihedral_angle_1_deg 5.383 r_angle_refined_deg 1.256 r_angle_other_deg 1.023 r_chiral_restr 0.066 r_bond_refined_d 0.013 r_bond_other_d 0.005 r_gen_planes_refined 0.005
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 28.87 r_dihedral_angle_4_deg 20.165 r_dihedral_angle_3_deg 14.129 r_dihedral_angle_1_deg 5.383 r_angle_refined_deg 1.256 r_angle_other_deg 1.023 r_chiral_restr 0.066 r_bond_refined_d 0.013 r_bond_other_d 0.005 r_gen_planes_refined 0.005 r_gen_planes_other 0.002
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3156 Nucleic Acid Atoms Solvent Atoms 44 Heterogen Atoms 58
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction