X-RAY DIFFRACTION

Starting Model(s)

Initial Refinement Model(s)
TypeSourceAccession CodeDetails
experimental modelPDB 1L6MPDB ENTRY 1L6M

Crystallization

Crystalization Experiments
IDMethodpHTemperatureDetails
1VAPOR DIFFUSION, HANGING DROP4.52911.3M Ammonium sulfate, 0.2M Lithium sulfate, 50mM sodium chloride, 0.1M sodium acetate, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Crystal Properties
Matthews coefficientSolvent content
2.957.53

Crystal Data

Unit Cell
Length ( Å )Angle ( ˚ )
a = 114.358α = 90
b = 114.358β = 90
c = 119.042γ = 90
Symmetry
Space GroupP 41 21 2

Diffraction

Diffraction Experiment
ID #Crystal IDScattering TypeData Collection TemperatureDetectorDetector TypeDetailsCollection DateMonochromatorProtocol
11x-ray100IMAGE PLATERIGAKU RAXIS IV2005-01-18MSINGLE WAVELENGTH
Radiation Source
ID #SourceTypeWavelength ListSynchrotron SiteBeamline
1ROTATING ANODERIGAKU RU2001.5418

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
12.57228.591000.0780.28912.6256552319463.391
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)
12.5722.661000.3977.112.52519

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 (Observed)R-WorkR-FreeR-Free Selection DetailsMean Isotropic B
X-RAY DIFFRACTIONUsed previously-determined structureTHROUGHOUTPDB ENTRY 1L6M2.57228.592565523194241099.720.248910.247510.26249Used same set as previously-determined structure46.342
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]
0.470.47-0.93
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.195
r_dihedral_angle_4_deg17.843
r_dihedral_angle_3_deg15.186
r_dihedral_angle_1_deg4.795
r_scangle_it0.991
r_angle_refined_deg0.84
r_angle_other_deg0.82
r_scbond_it0.668
r_mcangle_it0.582
r_mcbond_it0.456
RMS Deviations
KeyRefinement Restraint Deviation
r_dihedral_angle_2_deg36.195
r_dihedral_angle_4_deg17.843
r_dihedral_angle_3_deg15.186
r_dihedral_angle_1_deg4.795
r_scangle_it0.991
r_angle_refined_deg0.84
r_angle_other_deg0.82
r_scbond_it0.668
r_mcangle_it0.582
r_mcbond_it0.456
r_metal_ion_refined0.213
r_nbd_other0.207
r_symmetry_vdw_other0.188
r_nbtor_refined0.177
r_nbd_refined0.176
r_xyhbond_nbd_refined0.111
r_symmetry_vdw_refined0.101
r_mcbond_other0.09
r_nbtor_other0.078
r_symmetry_hbond_refined0.071
r_chiral_restr0.053
r_bond_refined_d0.006
r_bond_other_d0.006
r_gen_planes_refined0.002
r_gen_planes_other0.001
r_xyhbond_nbd_other
r_metal_ion_other
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen AtomsNumber
Protein Atoms4162
Nucleic Acid Atoms
Solvent Atoms78
Heterogen Atoms126

Software

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