4Y31

Crystal structure of yellow lupine LlPR-10.1A protein in ligand-free form


X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1ICX 

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP729218% PEG4000, 0.2 M sodium acetate, 0.1 M HEPES
Crystal Properties
Matthews coefficientSolvent content
1.8332.85

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 35.065α = 90
b = 56.501β = 90
c = 61.938γ = 90
Symmetry
Space GroupP 21 21 21

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100CCDMARMOSAIC 225 mm CCD2009-09-17MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1SYNCHROTRONBESSY BEAMLINE 14.10.91841BESSY14.1

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
11.323099.90.05919.73.729618
Highest Resolution Shell
ID #Resolution (High)Resolution (Low)Percent Possible (All)Percent Possible (Observed)Mean I Over Sigma (Observed)RedundancyNumber Unique Reflections (All)
11.321.3799.723.3

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 REPLACEMENTFREE R-VALUE1icx1.3228.2728503105999.70.152960.150760.21152RANDOM19.97
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]
-1.841.470.37
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.031
r_sphericity_free33.557
r_sphericity_bonded15.795
r_dihedral_angle_3_deg12.599
r_rigid_bond_restr7.261
r_dihedral_angle_1_deg7.109
r_angle_refined_deg1.818
r_angle_other_deg0.961
r_dihedral_angle_4_deg0.785
r_chiral_restr0.113
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg38.031
r_sphericity_free33.557
r_sphericity_bonded15.795
r_dihedral_angle_3_deg12.599
r_rigid_bond_restr7.261
r_dihedral_angle_1_deg7.109
r_angle_refined_deg1.818
r_angle_other_deg0.961
r_dihedral_angle_4_deg0.785
r_chiral_restr0.113
r_bond_refined_d0.019
r_gen_planes_refined0.01
r_gen_planes_other0.004
r_bond_other_d0.001
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_mcbond_it
r_mcbond_other
r_mcangle_it
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 Atoms1128
Nucleic Acid Atoms
Solvent Atoms177
Heterogen Atoms4

Software

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