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Crystal structure of human RAB43 in complex with GDP
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2EW1 PDB entry 2EW1
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 8.5 291 25% PEG8000, 0.2M NaCl, 0.1M Tris-HCl, pH 8.5, vapor diffusion, sitting drop, temperature 291K, VAPOR DIFFUSION, SITTING DROP
Crystal Properties Matthews coefficient Solvent content 2.8 55.2
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 66.447 α = 90 b = 66.447 β = 90 c = 145.116 γ = 120
Symmetry Space Group P 32 2 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 2006-06-27 M SINGLE WAVELENGTH 2 1
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE 1.54178
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 2.05 30 99.9 0.116 6.7 9.6 24106
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) 2.05 2.12 100 0.955 8.5
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-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R PDB entry 2EW1 2.05 20 23955 2019 99.688 0.237 0.2331 0.2346 0.2862 0.2816 thin shells 24.248
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] 0.984 0.492 0.984 -1.477
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.986 r_dihedral_angle_4_deg 16.568 r_dihedral_angle_3_deg 13.451 r_dihedral_angle_1_deg 6.13 r_mcangle_it 3.291 r_scangle_it 3.087 r_mcbond_it 2.402 r_scbond_it 2.377 r_angle_refined_deg 1.41 r_angle_other_deg 0.966
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 33.986 r_dihedral_angle_4_deg 16.568 r_dihedral_angle_3_deg 13.451 r_dihedral_angle_1_deg 6.13 r_mcangle_it 3.291 r_scangle_it 3.087 r_mcbond_it 2.402 r_scbond_it 2.377 r_angle_refined_deg 1.41 r_angle_other_deg 0.966 r_mcbond_other 0.715 r_symmetry_vdw_other 0.218 r_nbd_refined 0.209 r_nbd_other 0.199 r_nbtor_refined 0.175 r_symmetry_vdw_refined 0.164 r_symmetry_hbond_refined 0.157 r_xyhbond_nbd_refined 0.131 r_nbtor_other 0.085 r_chiral_restr 0.077 r_bond_refined_d 0.015 r_gen_planes_refined 0.005 r_bond_other_d 0.002 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2455 Nucleic Acid Atoms Solvent Atoms 76 Heterogen Atoms 61
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling PHASER phasing REFMAC refinement PDB_EXTRACT data extraction