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Crystal structure of the plant Rho protein ROP5
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 2NTY ROP4-GDP of model with PDB ID 2NTY
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5.5 293 28%(w/v) PEG 3000,
100 mM MES pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.07 40.63
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 36.42 α = 90 b = 40.39 β = 102.6 c = 57.18 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 CCD MARMOSAIC 225 mm CCD 2006-09-21 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X06SA 0.97634 SLS X06SA
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (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 1.53 50 2.9 23836
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1.53 1.6 1.9
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 ROP4-GDP of model with PDB ID 2NTY 1.53 24.72 22637 1191 100 0.24765 0.24673 0.2468 0.26504 0.2628 RANDOM 17.474
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] 0.01 -0.01
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.732 r_dihedral_angle_1_deg 27.915 r_dihedral_angle_4_deg 21.295 r_dihedral_angle_3_deg 16.466 r_scangle_it 3.923 r_scbond_it 2.739 r_angle_refined_deg 1.957 r_mcangle_it 1.838 r_mcbond_it 1.18 r_nbtor_refined 0.329
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.732 r_dihedral_angle_1_deg 27.915 r_dihedral_angle_4_deg 21.295 r_dihedral_angle_3_deg 16.466 r_scangle_it 3.923 r_scbond_it 2.739 r_angle_refined_deg 1.957 r_mcangle_it 1.838 r_mcbond_it 1.18 r_nbtor_refined 0.329 r_nbd_refined 0.24 r_symmetry_vdw_refined 0.238 r_chiral_restr 0.153 r_xyhbond_nbd_refined 0.152 r_symmetry_hbond_refined 0.114 r_bond_refined_d 0.027 r_gen_planes_refined 0.009 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_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_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1185 Nucleic Acid Atoms Solvent Atoms 48 Heterogen Atoms 29
Software Software Software Name Purpose REFMAC refinement