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GppNHp-Bound Ypt1p GTPase
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model Other Polyalanine Rab3A GTPase
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6.5 298 30% MPD, 10% Glycerol, 100mM MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal Properties Matthews coefficient Solvent content 2.08 40.43
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 39.011 α = 90 b = 56.93 β = 90 c = 74.72 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 IMAGE PLATE MAR scanner 300 mm plate osmic mirror 2003-07-01 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU RUH3R
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Sym 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 2.06 50 99.2 0.068 18.1 3 10706 10705 34.6
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.06 2.12 99.7 0.293 4.7 3 880
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-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 Polyalanine Rab3A GTPase 2.06 15 8258 514 99.3 0.212 0.19754 0.19562 0.1954 0.23462 0.234 RANDOM 27.148
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] -1.14 1.46 -0.32
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.337 r_dihedral_angle_4_deg 16.123 r_dihedral_angle_3_deg 15.622 r_dihedral_angle_1_deg 5.172 r_scangle_it 2.151 r_scbond_it 1.382 r_angle_refined_deg 1.174 r_mcangle_it 0.941 r_mcbond_it 0.511 r_nbtor_refined 0.303
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 35.337 r_dihedral_angle_4_deg 16.123 r_dihedral_angle_3_deg 15.622 r_dihedral_angle_1_deg 5.172 r_scangle_it 2.151 r_scbond_it 1.382 r_angle_refined_deg 1.174 r_mcangle_it 0.941 r_mcbond_it 0.511 r_nbtor_refined 0.303 r_symmetry_vdw_refined 0.234 r_nbd_refined 0.197 r_symmetry_hbond_refined 0.151 r_xyhbond_nbd_refined 0.134 r_metal_ion_refined 0.071 r_chiral_restr 0.069 r_bond_refined_d 0.008 r_gen_planes_refined 0.003 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_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 1391 Nucleic Acid Atoms Solvent Atoms 153 Heterogen Atoms 33
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing