3HD6

Crystal Structure of the Human Rhesus Glycoprotein RhCG


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 3B9W 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP8.52770.1M Tris pH 8.5 (at 293K), 40% PEG 200 + 20mM Tris pH 7.4 (at 293K), 100mM NaCl, 40mM BOG, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal Properties
Matthews coefficientSolvent content
2.6854.17

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 99.83α = 90
b = 99.83β = 90
c = 101.076γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDADSC QUANTUM 42008-12-08MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONALS BEAMLINE 8.3.11.11587ALS8.3.1

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
12.186.3999.70.0770.08939.710.633464334492
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)
12.12.1895.80.5890.6373.48.6

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT3B9W2.186.393346431746169599.680.169730.168370.19505RANDOM24.109
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]
0.690.340.69-1.03
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.159
r_dihedral_angle_3_deg12.602
r_dihedral_angle_4_deg9.676
r_dihedral_angle_1_deg5.133
r_scangle_it1.881
r_scbond_it1.204
r_angle_refined_deg1.018
r_angle_other_deg0.87
r_mcangle_it0.79
r_mcbond_it0.429
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.159
r_dihedral_angle_3_deg12.602
r_dihedral_angle_4_deg9.676
r_dihedral_angle_1_deg5.133
r_scangle_it1.881
r_scbond_it1.204
r_angle_refined_deg1.018
r_angle_other_deg0.87
r_mcangle_it0.79
r_mcbond_it0.429
r_mcbond_other0.095
r_chiral_restr0.066
r_bond_refined_d0.009
r_gen_planes_refined0.004
r_bond_other_d0.001
r_gen_planes_other0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3163
Nucleic Acid Atoms
Solvent Atoms116
Heterogen Atoms20

Software

Software
Software NamePurpose
ADSCdata collection
PHASERphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling