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RocCOR domain tandem of Rab family protein (Roco)
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3DPT PDB ENTRY 3DPT
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, SITTING DROP 7 293 0.1M HEPES (pH7.0), 1M Na citrate, VAPOR DIFFUSION, SITTING DROP, temperature 293K
Crystal Properties Matthews coefficient Solvent content 2.49 50.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 83.2 α = 90 b = 106.1 β = 90 c = 139 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 CCD MARRESEARCH 2007-09-29 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SLS BEAMLINE X10SA 0.97892 SLS X10SA
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 2.9 50 99 0.071 0.06 20.52 3.7 27740 27475 -3 51.197
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.9 3 99.7 0.466 0.398 4.2 3.7 2635
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) 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 THROUGHOUT PDB ENTRY 3DPT 2.9 47.67 -3 26101 1374 100 0.23226 0.23029 0.27005 0.2611 RANDOM 48.099
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] 2.68 -0.76 -1.93
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.169 r_dihedral_angle_3_deg 19.807 r_dihedral_angle_4_deg 18.064 r_dihedral_angle_1_deg 5.959 r_scangle_it 1.611 r_angle_refined_deg 1.3 r_scbond_it 0.951 r_mcangle_it 0.676 r_mcbond_it 0.374 r_nbtor_refined 0.313
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.169 r_dihedral_angle_3_deg 19.807 r_dihedral_angle_4_deg 18.064 r_dihedral_angle_1_deg 5.959 r_scangle_it 1.611 r_angle_refined_deg 1.3 r_scbond_it 0.951 r_mcangle_it 0.676 r_mcbond_it 0.374 r_nbtor_refined 0.313 r_nbd_refined 0.22 r_symmetry_hbond_refined 0.185 r_symmetry_vdw_refined 0.163 r_xyhbond_nbd_refined 0.151 r_chiral_restr 0.092 r_bond_refined_d 0.009 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_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 6235 Nucleic Acid Atoms Solvent Atoms Heterogen Atoms
Software Software Software Name Purpose REFMAC refinement XDS data reduction XSCALE data scaling PHASER phasing