4BVA

Crystal structure of the NADPH-T3 form of mouse Mu-crystallin.


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 2I99PDB ENTRY 2I99

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1200 MM KH2PO4, 15% PEG 3350, 280 MM NASCN
Crystal Properties
Matthews coefficientSolvent content
2.1642.48

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 45.24α = 90
b = 97.14β = 104.9
c = 75.67γ = 90
Symmetry
Space GroupP 1 21 1

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDADSC CCD2008-09-28MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONESRF BEAMLINE ID14-2ESRFID14-2

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
11.7542.799.50.0714.283.76636042
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)R Merge I (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.751.8598.70.43.693.74

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 2I991.7542.6860423318199.610.148570.146240.19224RANDOM18.677
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]
0.540.01-0.31-0.2
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.484
r_sphericity_free21.882
r_dihedral_angle_4_deg19.416
r_dihedral_angle_3_deg13.771
r_sphericity_bonded6.028
r_dihedral_angle_1_deg5.764
r_rigid_bond_restr1.673
r_mcangle_it1.477
r_angle_refined_deg1.28
r_mcbond_it1.185
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.484
r_sphericity_free21.882
r_dihedral_angle_4_deg19.416
r_dihedral_angle_3_deg13.771
r_sphericity_bonded6.028
r_dihedral_angle_1_deg5.764
r_rigid_bond_restr1.673
r_mcangle_it1.477
r_angle_refined_deg1.28
r_mcbond_it1.185
r_mcbond_other1.178
r_angle_other_deg0.734
r_chiral_restr0.067
r_bond_refined_d0.007
r_gen_planes_refined0.005
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_mcangle_other
r_scbond_it
r_scbond_other
r_scangle_it
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4561
Nucleic Acid Atoms
Solvent Atoms538
Heterogen Atoms144

Software

Software
Software NamePurpose
REFMACrefinement
XDSdata reduction
XDSdata scaling
PHASERphasing