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High resolution crystal structure of human Rab9 GTPase: a novel antiviral drug target
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1OIV PDB entry 1OIV
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 5 277 PEG4000, sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 2.02 39.04
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.4 α = 99.75 b = 45.62 β = 107.17 c = 51.22 γ = 101.84
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 2004-03-22 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON APS BEAMLINE 22-ID 1.0000 APS 22-ID
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 1.25 50 84.7 0.063 0.063 25.5 6.9 73993 73993
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) 1.25 1.29 39.9 0.392 0.392 2.3
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB entry 1OIV 1.25 10 73767 73767 3697 84.7 0.141 0.139 0.139 0.1445 0.196 Random
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]
Coordinate Error Structure Solution Method Refinement High Resolution Refinement Low Resolution 2552 3229
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.086 s_non_zero_chiral_vol 0.072 s_zero_chiral_vol 0.064 s_similar_adp_cmpnt 0.056 s_anti_bump_dis_restr 0.05 s_angle_d 0.032 s_from_restr_planes 0.027 s_bond_d 0.013 s_rigid_bond_adp_cmpnt 0.004 s_similar_dist
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 2662 Nucleic Acid Atoms Solvent Atoms 508 Heterogen Atoms 56
Software Software Software Name Purpose HKL-2000 data collection SCALEPACK data scaling CNS refinement SHELXL refinement HKL-2000 data reduction CNS phasing