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Crystal Structure of Human Rab5a GTPase Domain at 1.05 A resolution
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1N6N PDB ENTRY 1N6N
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 6 277 PEG 6000, SODIUM CHLORIDE, MES, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties Matthews coefficient Solvent content 1.73 29.1
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 35.727 α = 90 b = 64.573 β = 90 c = 66.18 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 ADSC QUANTUM 4 2002-07-17 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON CHESS BEAMLINE F1 0.916 CHESS F1
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 1.05 29.02 95.2 0.065 18.7 4.8 68904 68904 -3 10.2
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 1.05 1.07 79 0.52 2.2 3050
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 (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION FOURIER SYNTHESIS THROUGHOUT PDB ENTRY 1N6N 1.05 29.02 68700 68700 2063 95 0.125 0.124 0.1239 0.13 0.1688 0.1436 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 55 1293 1593.9
RMS Deviations Key Refinement Restraint Deviation s_approx_iso_adps 0.109 s_non_zero_chiral_vol 0.098 s_zero_chiral_vol 0.082 s_anti_bump_dis_restr 0.068 s_similar_adp_cmpnt 0.065 c_angle_d 0.036 s_from_restr_planes 0.0288 c_bond_d 0.015 s_rigid_bond_adp_cmpnt 0.005
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1335 Nucleic Acid Atoms Solvent Atoms 213 Heterogen Atoms 69
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling CNS refinement SHELXL-97 refinement CNS phasing