2R16

Crystal Structure of bovine neurexin 1 alpha LNS/LG domain 4 (with no splice insert)


X-RAY DIFFRACTION

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP929312.5% isopropanol, 0.1 M CHES pH 9.0, 5 mM CaCl2, , VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal Properties
Matthews coefficientSolvent content
2.2745.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 90.322α = 90
b = 90.322β = 90
c = 39.624γ = 120
Symmetry
Space GroupP 63

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray103CCDMARMOSAIC 300 mm CCD2006-08-16MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONAPS BEAMLINE 23-ID-B0.96112APS23-ID-B

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
11.0423.792.90.0737.912.682197821977.5
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)
1.041.0860.50.2960.2966.27.65319

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 REPLACEMENTTHROUGHOUTPDB entry 1C4R1.0423.7808717276381081000.148390.148390.14650.16518RANDOM11.292
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]
-0.08-0.04-0.080.13
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.14
r_dihedral_angle_3_deg12.328
r_dihedral_angle_4_deg10.121
r_sphericity_free8.859
r_dihedral_angle_1_deg7.896
r_scangle_it3.966
r_sphericity_bonded3.947
r_scbond_it2.964
r_mcangle_it2.35
r_angle_other_deg1.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg31.14
r_dihedral_angle_3_deg12.328
r_dihedral_angle_4_deg10.121
r_sphericity_free8.859
r_dihedral_angle_1_deg7.896
r_scangle_it3.966
r_sphericity_bonded3.947
r_scbond_it2.964
r_mcangle_it2.35
r_angle_other_deg1.93
r_angle_refined_deg1.906
r_mcbond_it1.659
r_rigid_bond_restr1.389
r_mcbond_other0.68
r_symmetry_hbond_refined0.425
r_symmetry_vdw_other0.332
r_nbd_refined0.226
r_nbd_other0.217
r_symmetry_vdw_refined0.215
r_nbtor_refined0.175
r_xyhbond_nbd_refined0.136
r_chiral_restr0.115
r_nbtor_other0.094
r_metal_ion_refined0.06
r_bond_refined_d0.016
r_gen_planes_refined0.008
r_bond_other_d0.002
r_gen_planes_other0.002
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms1476
Nucleic Acid Atoms
Solvent Atoms130
Heterogen Atoms1

Software

Software
Software NamePurpose
REFMACrefinement
CNSrefinement
MAR345data collection
HKL-2000data reduction
HKL-2000data scaling
CNSphasing