2A5J | pdb_00002a5j

Crystal Structure of Human RAB2B


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1OIVPDB ENTRY 1OIV

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION6.530030% PEG5000, 02M Ammonium Sulfate, 0.1M MES, pH 6.5, VAPOR DIFFUSION, temperature 300K
Crystal Properties
Matthews coefficientSolvent content
2.141.9

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 44.104α = 90
b = 54.732β = 90
c = 70.765γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDSBC-3mirrors2005-06-29MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 19-BM0.966APS19-BM

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)RedundancyNumber Reflections (All)Number Reflections (Observed)Observed Criterion Sigma (F)Observed Criterion Sigma (I)B (Isotropic) From Wilson Plot
11.524.697.70.0460.04611.86.4274732747315.4
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)RedundancyNumber Unique Reflections (All)
1.51.53810.4190.4192.93.31127

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-Work (Depositor)R-Work (DCC)R-Free (Depositor)R-Free (DCC)R-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUTPDB ENTRY 1OIV1.50124.6265432654387897.660.196110.196110.195180.190.224660.22RANDOM17.043
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]
-0.240.040.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.953
r_dihedral_angle_4_deg17.448
r_dihedral_angle_3_deg11.693
r_dihedral_angle_1_deg5.464
r_scangle_it3.133
r_scbond_it2.004
r_mcangle_it1.364
r_angle_refined_deg1.285
r_mcbond_it0.872
r_nbtor_refined0.307
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg32.953
r_dihedral_angle_4_deg17.448
r_dihedral_angle_3_deg11.693
r_dihedral_angle_1_deg5.464
r_scangle_it3.133
r_scbond_it2.004
r_mcangle_it1.364
r_angle_refined_deg1.285
r_mcbond_it0.872
r_nbtor_refined0.307
r_nbd_refined0.202
r_symmetry_vdw_refined0.195
r_symmetry_hbond_refined0.157
r_xyhbond_nbd_refined0.127
r_chiral_restr0.074
r_bond_refined_d0.009
r_gen_planes_refined0.005
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 AtomsNumber
Protein Atoms1415
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms29

Software

Software
Software NamePurpose
REFMACrefinement
SBC-Collectdata collection
HKL-2000data scaling
MOLREPphasing