3REZ

glycoprotein GPIb variant


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, SITTING DROP52920.1 M MMT buffer pH 5 (MMT buffer is a mixture of DL-malic acid, MES and Tris base in the molar ratios 1:2:2 DL-malic acid:MES:Tris base), 25% (w/v) PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 292K
Crystal Properties
Matthews coefficientSolvent content
2.2846.08

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 72.01α = 90
b = 72.01β = 90
c = 171.731γ = 120
Symmetry
Space GroupP 31 2 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray80CCDMARC MOSAIC32010-06-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID290.8726ESRFID29

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (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
12.262.3610023135

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodResolution (High)Resolution (Low)Number Reflections (Observed)Number Reflections (R-Free)Percent Reflections (Observed)R-Factor (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONMOLECULAR REPLACEMENTTHROUGHOUT2.3542.1719566103692.530.21390.211460.25925RANDOM26.575
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]
-0.03-0.01-0.030.04
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.855
r_dihedral_angle_3_deg16.11
r_dihedral_angle_4_deg13.386
r_dihedral_angle_1_deg5.449
r_scangle_it1.487
r_angle_refined_deg1.301
r_scbond_it0.836
r_mcangle_it0.35
r_mcbond_it0.178
r_chiral_restr0.073
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.855
r_dihedral_angle_3_deg16.11
r_dihedral_angle_4_deg13.386
r_dihedral_angle_1_deg5.449
r_scangle_it1.487
r_angle_refined_deg1.301
r_scbond_it0.836
r_mcangle_it0.35
r_mcbond_it0.178
r_chiral_restr0.073
r_bond_refined_d0.007
r_gen_planes_refined0.004
r_bond_other_d
r_angle_other_deg
r_gen_planes_other
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_mcbond_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms3473
Nucleic Acid Atoms
Solvent Atoms273
Heterogen Atoms118

Software

Software
Software NamePurpose
PHASERphasing
REFMACrefinement
MOSFLMdata reduction
SCALAdata scaling