X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelOtherRab3a polyalanine

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP6277Ammonium sulfate, MES, Glycerol, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6954

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 68.808α = 90
b = 68.808β = 90
c = 90.92γ = 90
Symmetry
Space GroupP 43 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMAR scanner 300 mm plate2002-11-23MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RUH3R

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Sym I (Observed)Net I Over Average Sigma (I)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
12.055098.90.07815.141380311
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R-Sym I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
12.052.1198.90.2824.142011

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (High)Resolution (Low)Number Reflections (All)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (All)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTRab3a polyalanine2.077252091265666598.580.1790.15820.156310.19547Random16.527
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]
0.150.15-0.3
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.178
r_dihedral_angle_4_deg15.99
r_dihedral_angle_3_deg13.098
r_dihedral_angle_1_deg6.016
r_scangle_it2.425
r_scbond_it1.543
r_angle_refined_deg1.222
r_mcangle_it0.963
r_mcbond_it0.876
r_angle_other_deg0.795
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.178
r_dihedral_angle_4_deg15.99
r_dihedral_angle_3_deg13.098
r_dihedral_angle_1_deg6.016
r_scangle_it2.425
r_scbond_it1.543
r_angle_refined_deg1.222
r_mcangle_it0.963
r_mcbond_it0.876
r_angle_other_deg0.795
r_nbd_refined0.204
r_symmetry_vdw_other0.186
r_nbd_other0.182
r_nbtor_refined0.176
r_symmetry_hbond_refined0.176
r_xyhbond_nbd_refined0.157
r_symmetry_vdw_refined0.136
r_mcbond_other0.115
r_nbtor_other0.081
r_chiral_restr0.071
r_metal_ion_refined0.037
r_bond_refined_d0.008
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1384
Nucleic Acid Atoms
Solvent Atoms237
Heterogen Atoms43

Software

Software
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
REFMACrefinement