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high resolution structure of GppNHp-bound human Rab4a
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1HUQ PDB ENTRY 1HUQ
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 298 8% (W/V) PEG 4000, 100MM SODIUM ACETATE PH 4.0 HANGING DROP 25 DEGREE CELSIUS
Crystal Properties Matthews coefficient Solvent content 2.65 53.24
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 99.79 α = 90 b = 99.79 β = 90 c = 95.54 γ = 90
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 CCD MIRROR 2002-11-23 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-4 ESRF ID14-4
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 1.6 20 99.5 0.06 20.9 6.9 128819
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 1.6 1.75 97.4 0.25 6.7
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 PDB ENTRY 1HUQ 1.57 19.54 122377 6441 100 0.194 0.192 0.2043 0.229 0.233 RANDOM 15.9
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] 0.45 0.45 -0.89
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.038 r_scangle_it 4.205 r_scbond_it 2.709 r_angle_refined_deg 1.821 r_mcangle_it 1.658 r_mcbond_it 1.022 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.148
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_1_deg 6.038 r_scangle_it 4.205 r_scbond_it 2.709 r_angle_refined_deg 1.821 r_mcangle_it 1.658 r_mcbond_it 1.022 r_symmetry_vdw_refined 0.242 r_nbd_refined 0.21 r_xyhbond_nbd_refined 0.149 r_symmetry_hbond_refined 0.148 r_chiral_restr 0.124 r_bond_refined_d 0.018 r_gen_planes_refined 0.009 r_bond_other_d r_angle_other_deg r_dihedral_angle_2_deg r_dihedral_angle_3_deg r_dihedral_angle_4_deg r_gen_planes_other r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_other r_metal_ion_refined 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_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 5532 Nucleic Acid Atoms Solvent Atoms 684 Heterogen Atoms 172
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling MOLREP phasing