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Crystal structure of a predicted human GTPase in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G17 PDB entry 1G17, chain A
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 5 291 22% PEG4000, 0.2M calcium acetate, 0.1M sodium cacodylate, pH 5.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K
Crystal Properties Matthews coefficient Solvent content 2.5 51.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 45.463 α = 90 b = 45.463 β = 90 c = 315.454 γ = 120
Symmetry Space Group P 65 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 100 CCD MARMOSAIC 300 mm CCD 2006-07-15 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 0.97625 APS 22-ID
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 50 94.2 0.052 13.1 13.9 13543
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 2.07 52.3 0.43 2.1
Refinement Statistics Diffraction ID Structure Solution Method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT PDB entry 1G17, chain A 2.1 30 12316 615 99.467 0.2412 0.2553 0.2661 0.2809 39.449
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] -0.056 -0.028 -0.056 0.085
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.483 r_dihedral_angle_4_deg 15.609 r_dihedral_angle_3_deg 13.407 r_dihedral_angle_1_deg 5.825 r_scangle_it 3.6 r_mcangle_it 3.245 r_scbond_it 2.74 r_mcbond_it 2.439 r_angle_refined_deg 1.415 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 37.483 r_dihedral_angle_4_deg 15.609 r_dihedral_angle_3_deg 13.407 r_dihedral_angle_1_deg 5.825 r_scangle_it 3.6 r_mcangle_it 3.245 r_scbond_it 2.74 r_mcbond_it 2.439 r_angle_refined_deg 1.415 r_nbtor_refined 0.294 r_symmetry_vdw_refined 0.241 r_metal_ion_refined 0.221 r_nbd_refined 0.206 r_symmetry_hbond_refined 0.154 r_xyhbond_nbd_refined 0.143 r_chiral_restr 0.094 r_symmetry_metal_ion_refined 0.092 r_bond_refined_d 0.016 r_gen_planes_refined 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1278 Nucleic Acid Atoms Solvent Atoms 24 Heterogen Atoms 36
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing PDB_EXTRACT data extraction HKL-2000 data scaling REFMAC refinement ARP/wARP model building MolProbity model building Coot model building