1GSM

A reassessment of the MAdCAM-1 structure and its role in integrin recognition.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1BQSPDB ENTRY 1BQS

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
18PROTEIN SOLUTION:10 MG/ML. CRYSTALLIZATION SOLUTION: 16% PEG 4000, 0.5M LI2SO4, PH 7.75.
Crystal Properties
Matthews coefficientSolvent content
2.5143.3

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 64α = 90
b = 99.2β = 90
c = 70.5γ = 90
Symmetry
Space GroupC 2 2 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATEMARRESEARCHMSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONEMBL/DESY, HAMBURG BEAMLINE X11EMBL/DESY, HAMBURGX11

Data Collection

Overall
ID #Resolution (High)Resolution (Low)Percent Possible (Observed)R Merge 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
11.930990.03343.34.81025743

Refinement

Statistics
Diffraction IDStructure Solution MethodCross Validation methodStarting modelResolution (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 REPLACEMENTTHROUGHOUTPDB ENTRY 1BQS1.929.491676490197.90.2180.2170.25RANDOM
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]
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.763
r_scbond_it2.885
r_mcangle_it1.935
r_angle_other_deg1.858
r_mcbond_it1.063
r_symmetry_hbond_refined0.307
r_nbd_refined0.225
r_symmetry_vdw_refined0.224
r_xyhbond_nbd_refined0.182
r_chiral_restr0.116
RMS Deviations
KeyRefinement Restraint Deviation
r_scangle_it4.763
r_scbond_it2.885
r_mcangle_it1.935
r_angle_other_deg1.858
r_mcbond_it1.063
r_symmetry_hbond_refined0.307
r_nbd_refined0.225
r_symmetry_vdw_refined0.224
r_xyhbond_nbd_refined0.182
r_chiral_restr0.116
r_bond_refined_d0.014
r_gen_planes_refined0.007
r_bond_other_d
r_angle_refined_deg
r_dihedral_angle_1_deg
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_gen_planes_other
r_nbd_other
r_nbtor_refined
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_mcangle_other
r_scbond_other
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1531
Nucleic Acid Atoms
Solvent Atoms184
Heterogen Atoms

Software

Software
Software NamePurpose
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing