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Crystal structure of Rab GTPase Sec4p mutant - S29V
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1G16
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 BATCH MODE 293.15 After initial crystal screening, small crystals were obtained in 14% PEG3350, 200mM Zinc Acetate. After refinement, large single crystals were obtained in 14% PEG4000, 50mM Zinc Acetate.
Crystal Properties Matthews coefficient Solvent content 2.07 40.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 31.72 α = 90 b = 75.45 β = 91.58 c = 66.23 γ = 90
Symmetry Space Group P 1 21 1
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 RIGAKU RAXIS IV++ 2008-12-13 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE RIGAKU 1.5418
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (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 1.87 66.2 94.8 0.052 0.052 9.1 1.7 23244 2 23.5
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 1.87 2 98.3 0.285 2.3 1.6
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-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 1G16 1.9 28.3 21712 1170 92.83 0.23874 0.23553 0.2984 0.3021 RANDOM 22.195
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] -0.03 0.04 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.189 r_dihedral_angle_3_deg 18.878 r_dihedral_angle_4_deg 16.805 r_dihedral_angle_1_deg 6.493 r_angle_refined_deg 1.61 r_chiral_restr 0.111 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 39.189 r_dihedral_angle_3_deg 18.878 r_dihedral_angle_4_deg 16.805 r_dihedral_angle_1_deg 6.493 r_angle_refined_deg 1.61 r_chiral_restr 0.111 r_bond_refined_d 0.011 r_gen_planes_refined 0.006 r_bond_other_d r_angle_other_deg r_gen_planes_other r_nbd_refined r_nbd_other r_nbtor_refined r_nbtor_other r_xyhbond_nbd_refined r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_vdw_refined r_symmetry_vdw_other r_symmetry_hbond_refined r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_it r_mcbond_other r_mcangle_it r_mcangle_other r_scbond_it r_scbond_other r_scangle_it 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 2591 Nucleic Acid Atoms Solvent Atoms 345 Heterogen Atoms 61
Software Software Software Name Purpose REFMAC refinement MOSFLM data reduction SCALA data scaling PHASER phasing